Sodium in PDB 7wu1: Crystal Structure of Phospholipase D From Moritella Sp. JT01

All present enzymatic activity of Crystal Structure of Phospholipase D From Moritella Sp. JT01:
3.1.4.4;

The structure of Crystal Structure of Phospholipase D From Moritella Sp. JT01, PDB code: 7wu1 was solved by Y.H.Wang, X.J.Mao, J.Wang, F.H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.897, 216.644, 277.708, 90, 90, 90
R / Rfree (%)	21.2 / 21.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 47;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Phospholipase D From Moritella Sp. JT01 (pdb code 7wu1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 47 binding sites of Sodium where determined in the Crystal Structure of Phospholipase D From Moritella Sp. JT01, PDB code: 7wu1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:57.8 occ:1.00 HB3 A:PRO286 2.6 59.8 1.0 OH A:TYR60 2.7 50.2 1.0 O A:GLN283 2.7 58.5 1.0 HA A:LEU282 2.8 56.8 1.0 HE2 A:TYR60 2.9 66.4 1.0 O A:TYR281 2.9 53.2 1.0 HZ A:PHE64 3.0 63.4 1.0 H A:GLN283 3.2 60.8 1.0 HG3 A:PRO286 3.2 61.4 1.0 N A:GLN283 3.3 57.2 1.0 HH A:TYR60 3.3 59.0 1.0 C A:LEU282 3.4 50.5 1.0 CB A:PRO286 3.5 50.7 1.0 CA A:LEU282 3.5 49.1 1.0 CE2 A:TYR60 3.5 54.2 1.0 CZ A:TYR60 3.6 51.5 1.0 C A:GLN283 3.7 58.0 1.0 HD3 A:PRO286 3.7 58.9 1.0 CZ A:PHE64 3.7 53.2 1.0 CG A:PRO286 3.8 52.3 1.0 C A:TYR281 3.8 52.8 1.0 HG21 A:VAL112 3.8 59.8 1.0 HE2 A:PHE64 3.9 66.5 1.0 HB3 A:ALA114 3.9 61.2 1.0 N A:LEU282 3.9 49.5 1.0 HB2 A:PRO286 4.0 59.8 1.0 CA A:GLN283 4.0 57.8 1.0 O A:LEU282 4.0 50.7 1.0 HA A:GLN283 4.2 62.5 1.0 CE2 A:PHE64 4.2 55.0 1.0 CD A:PRO286 4.2 50.3 1.0 O A:HOH742 4.2 51.0 1.0 HB2 A:ALA114 4.4 61.2 1.0 CB A:ALA114 4.5 59.1 1.0 HA A:PRO286 4.5 62.3 1.0 CA A:PRO286 4.6 51.1 1.0 H A:LEU282 4.6 58.9 1.0 HG2 A:PRO286 4.6 61.4 1.0 HB1 A:ALA114 4.6 61.2 1.0 CG2 A:VAL112 4.6 50.0 1.0 HD23 A:LEU282 4.7 57.8 1.0 HG23 A:VAL112 4.7 59.8 1.0 CE1 A:PHE64 4.8 51.1 1.0 N A:PRO286 4.8 51.0 1.0 CB A:LEU282 4.8 48.8 1.0 HE1 A:PHE64 4.9 59.9 1.0 CD2 A:TYR60 4.9 53.6 1.0 CE1 A:TYR60 4.9 52.4 1.0 N A:ARG284 4.9 55.2 1.0 HB3 A:LEU282 4.9 56.9 1.0 O A:HOH816 4.9 52.0 1.0

Sodium binding site 2 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:63.2 occ:1.00 H A:PHE51 2.2 63.0 1.0 HA A:HIS50 2.7 64.7 1.0 O A:PRO286 2.7 52.3 1.0 HB2 A:HIS50 3.0 62.6 1.0 HB2 A:ASN288 3.0 58.6 1.0 N A:PHE51 3.0 50.7 1.0 HG2 A:PRO286 3.1 61.4 1.0 CD2 A:PHE51 3.2 53.2 1.0 CE2 A:PHE51 3.2 54.6 1.0 CG A:PHE51 3.3 53.0 1.0 CZ A:PHE51 3.3 55.0 1.0 CD1 A:PHE51 3.3 52.2 1.0 CA A:HIS50 3.3 56.6 1.0 CE1 A:PHE51 3.4 52.6 1.0 HB3 A:HIS50 3.4 62.6 1.0 CB A:HIS50 3.4 55.7 1.0 N A:ASN288 3.4 55.2 1.0 H A:ASN288 3.5 57.5 1.0 HA A:ASN288 3.5 60.3 1.0 C A:PRO286 3.6 50.5 1.0 HD2 A:PHE51 3.7 64.8 1.0 C A:HIS50 3.7 56.4 1.0 HB2 A:PRO286 3.7 59.8 1.0 HE2 A:PHE51 3.7 67.7 1.0 CA A:ASN288 3.8 56.9 1.0 CB A:ASN288 3.8 57.0 1.0 C A:VAL287 3.8 50.1 1.0 HZ A:PHE51 3.8 69.0 1.0 HD1 A:PHE51 3.8 63.8 1.0 HE1 A:PHE51 3.9 64.5 1.0 CG A:PRO286 4.0 52.3 1.0 HA A:VAL287 4.1 57.8 1.0 CB A:PHE51 4.1 54.0 1.0 CA A:PHE51 4.1 52.1 1.0 CB A:PRO286 4.2 50.7 1.0 O A:VAL287 4.2 50.0 1.0 HB3 A:ASN288 4.2 58.6 1.0 HB3 A:PHE51 4.3 66.9 1.0 NA A:NA611 4.3 65.5 1.0 O A:MET496 4.3 55.0 1.0 CA A:VAL287 4.3 49.5 1.0 N A:VAL287 4.3 48.6 1.0 CA A:PRO286 4.5 51.1 1.0 HG3 A:PRO286 4.6 61.4 1.0 N A:HIS50 4.7 55.6 1.0 HD11 A:ILE486 4.7 67.3 1.0 HA A:PHE51 4.8 64.1 1.0 CG A:HIS50 4.9 55.7 1.0 O A:HIS50 4.9 57.9 1.0 O A:THR49 4.9 51.7 1.0 O A:PHE51 4.9 53.3 1.0 CG A:ASN288 4.9 57.7 1.0 N A:PRO286 4.9 51.0 1.0 HD2 A:PRO286 4.9 58.9 1.0 CD A:PRO286 5.0 50.3 1.0 HB2 A:PHE51 5.0 66.9 1.0

Sodium binding site 3 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:63.1 occ:1.00 O A:VAL287 2.6 50.0 1.0 OG1 A:THR49 2.7 51.0 1.0 HB A:THR49 2.8 55.5 1.0 HB2 A:PRO286 2.9 59.8 1.0 HD1 A:TYR281 3.0 60.9 1.0 O A:THR49 3.0 51.7 1.0 C A:THR49 3.0 53.3 1.0 HA A:TYR281 3.1 57.9 1.0 HB3 A:TYR281 3.1 58.4 1.0 O A:TYR281 3.1 53.2 1.0 HA A:HIS50 3.2 64.7 1.0 CB A:THR49 3.2 49.6 1.0 HG1 A:THR49 3.2 59.8 1.0 N A:HIS50 3.3 55.6 1.0 CA A:TYR281 3.7 51.5 1.0 H A:HIS50 3.7 63.2 1.0 CA A:HIS50 3.7 56.6 1.0 CA A:THR49 3.7 52.4 1.0 CB A:PRO286 3.7 50.7 1.0 CB A:TYR281 3.8 51.5 1.0 HB3 A:PRO286 3.8 59.8 1.0 C A:VAL287 3.8 50.1 1.0 CD1 A:TYR281 3.8 52.8 1.0 C A:TYR281 3.8 52.8 1.0 HA A:ASN288 3.8 60.3 1.0 HB1 A:ALA114 4.1 61.2 1.0 CG A:TYR281 4.3 49.4 1.0 H A:ASP289 4.3 61.3 1.0 HA A:THR49 4.3 60.9 1.0 HB2 A:ALA114 4.3 61.2 1.0 N A:VAL287 4.4 48.6 1.0 H A:VAL287 4.4 56.9 1.0 HD23 A:LEU282 4.5 57.8 1.0 C A:HIS50 4.5 56.4 1.0 C A:PRO286 4.6 50.5 1.0 CA A:ASN288 4.6 56.9 1.0 N A:ASN288 4.6 55.2 1.0 CG2 A:THR49 4.6 50.5 1.0 CA A:PRO286 4.6 51.1 1.0 HB2 A:TYR281 4.6 58.4 1.0 CB A:ALA114 4.7 59.1 1.0 HG21 A:THR49 4.7 57.1 1.0 HA A:PRO286 4.7 62.3 1.0 CA A:VAL287 4.7 49.5 1.0 N A:ASP289 4.7 60.9 1.0 H A:THR49 4.8 60.7 1.0 HB3 A:HIS50 4.8 62.6 1.0 N A:THR49 4.8 52.0 1.0 NE2 A:HIS274 4.9 54.4 1.0 CE1 A:TYR281 4.9 52.8 1.0 CG A:PRO286 4.9 52.3 1.0 CB A:HIS50 4.9 55.7 1.0 O A:ASP280 4.9 57.8 1.0 HG2 A:PRO286 5.0 61.4 1.0 HE1 A:TYR281 5.0 61.7 1.0

Sodium binding site 4 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:65.6 occ:1.00 HE2 A:MET78 2.3 77.9 1.0 OD1 A:ASP115 2.5 55.0 1.0 O A:LEU282 2.8 50.7 1.0 HB3 A:LEU282 2.9 56.9 1.0 HE1 A:PHE64 3.0 59.9 1.0 HG22 A:VAL112 3.1 59.8 1.0 OD2 A:ASP115 3.1 56.5 1.0 HG2 A:MET78 3.2 73.3 1.0 CG A:ASP115 3.2 57.1 1.0 CE A:MET78 3.2 70.2 1.0 HG3 A:MET78 3.5 73.3 1.0 CG A:MET78 3.6 68.5 1.0 NA A:NA608 3.6 59.0 1.0 SD A:MET78 3.6 71.0 1.0 CB A:LEU282 3.8 48.8 1.0 HE3 A:MET78 3.8 77.9 1.0 C A:LEU282 3.8 50.5 1.0 HE1 A:MET78 3.8 77.9 1.0 CE1 A:PHE64 3.8 51.1 1.0 CG2 A:VAL112 3.8 50.0 1.0 HG21 A:VAL112 3.9 59.8 1.0 HZ A:PHE64 3.9 63.4 1.0 HA A:LEU282 4.0 56.8 1.0 HG23 A:VAL112 4.1 59.8 1.0 CA A:LEU282 4.1 49.1 1.0 HB2 A:LEU282 4.1 56.9 1.0 HD22 A:LEU282 4.2 57.8 1.0 CZ A:PHE64 4.3 53.2 1.0 H A:VAL112 4.3 61.0 1.0 HD13 A:LEU282 4.4 60.5 1.0 HA A:THR111 4.6 67.8 1.0 CB A:ASP115 4.7 55.9 1.0 CG A:LEU282 4.8 50.0 1.0 HA A:GLN283 4.8 62.5 1.0 HG13 A:VAL112 4.9 63.6 1.0 H A:ASP115 4.9 56.8 1.0 CD1 A:PHE64 4.9 52.9 1.0 N A:GLN283 4.9 57.2 1.0 CD2 A:LEU282 5.0 50.4 1.0 HA A:ASP115 5.0 60.9 1.0 N A:VAL112 5.0 52.6 1.0 HD1 A:PHE64 5.0 63.6 1.0

Sodium binding site 5 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:43.5 occ:1.00 HD22 A:ASN515 2.4 61.0 1.0 HG A:SER519 2.4 60.8 1.0 HE22 A:GLN523 2.4 62.0 1.0 HD12 A:LEU521 2.8 60.7 1.0 OG A:SER519 3.1 54.7 1.0 O A:HOH762 3.1 57.7 1.0 NE2 A:GLN523 3.1 55.6 1.0 ND2 A:ASN515 3.2 52.5 1.0 O A:HOH768 3.3 54.6 1.0 HE21 A:GLN523 3.3 62.0 1.0 HB3 A:SER519 3.3 62.7 1.0 HD21 A:ASN515 3.4 61.0 1.0 HB2 A:ASN515 3.7 63.3 1.0 CB A:SER519 3.7 56.4 1.0 HB2 A:LEU521 3.7 59.3 1.0 CD1 A:LEU521 3.7 50.7 1.0 ND1 A:HIS258 3.9 51.8 1.0 H A:ASN515 3.9 60.7 1.0 CE1 A:HIS258 4.0 52.8 1.0 HG A:LEU521 4.0 60.5 1.0 HE1 A:TYR517 4.0 63.7 1.0 HB2 A:SER519 4.0 62.7 1.0 HH A:TYR517 4.1 62.1 1.0 HD1 A:HIS258 4.1 57.5 1.0 HD11 A:LEU521 4.1 60.7 1.0 CG A:HIS258 4.1 52.4 1.0 NE2 A:HIS258 4.2 51.1 1.0 CG A:ASN515 4.2 53.3 1.0 HE1 A:HIS258 4.2 59.3 1.0 CD2 A:HIS258 4.3 52.6 1.0 CG A:LEU521 4.3 51.0 1.0 CD A:GLN523 4.3 55.1 1.0 HD13 A:LEU521 4.4 60.7 1.0 CE1 A:TYR517 4.4 55.4 1.0 O A:HOH746 4.4 53.8 1.0 OH A:TYR517 4.4 53.1 1.0 CB A:ASN515 4.4 54.7 1.0 CB A:LEU521 4.5 50.0 1.0 CZ A:TYR517 4.5 53.3 1.0 HB2 A:HIS258 4.6 58.8 1.0 HB3 A:HIS258 4.6 58.8 1.0 HD2 A:HIS514 4.7 65.1 1.0 N A:ASN515 4.7 52.6 1.0 OE1 A:GLN523 4.7 54.4 1.0 H A:LEU521 4.8 58.9 1.0 O A:HOH774 4.8 58.0 1.0 HD2 A:HIS258 4.8 59.2 1.0 CB A:HIS258 4.8 52.4 1.0 HA A:HIS514 4.9 62.1 1.0

Sodium binding site 6 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:59.0 occ:1.00 O A:HOH760 2.7 50.6 1.0 O A:PHE76 2.8 53.8 1.0 HB2 A:LEU282 2.8 56.9 1.0 O A:LEU282 2.9 50.7 1.0 HB2 A:ALA153 2.9 58.7 1.0 HB2 A:ASN77 3.1 61.5 1.0 HB3 A:LEU282 3.2 56.9 1.0 HG2 A:GLN283 3.2 61.4 1.0 HB3 A:ALA153 3.4 58.7 1.0 HE2 A:MET78 3.4 77.9 1.0 CB A:LEU282 3.4 48.8 1.0 HG3 A:GLN283 3.5 61.4 1.0 HE21 A:GLN283 3.6 61.5 1.0 CB A:ALA153 3.6 53.8 1.0 HE3 A:MET78 3.6 77.9 1.0 NA A:NA606 3.6 65.6 1.0 HG3 A:MET78 3.7 73.3 1.0 HD22 A:ASN77 3.7 67.8 1.0 C A:LEU282 3.7 50.5 1.0 CG A:GLN283 3.8 55.7 1.0 C A:PHE76 3.9 55.1 1.0 CE A:MET78 4.0 70.2 1.0 H A:ALA153 4.0 58.1 1.0 HD12 A:LEU282 4.0 60.5 1.0 CB A:ASN77 4.0 58.3 1.0 HB1 A:ALA153 4.1 58.7 1.0 CA A:LEU282 4.2 49.1 1.0 NE2 A:GLN283 4.3 54.3 1.0 O A:ASN77 4.3 62.6 1.0 HD13 A:LEU282 4.3 60.5 1.0 HE1 A:PHE64 4.4 59.9 1.0 HB3 A:ASN77 4.4 61.5 1.0 ND2 A:ASN77 4.5 60.4 1.0 CD1 A:LEU282 4.5 50.1 1.0 CG A:MET78 4.5 68.5 1.0 CD A:GLN283 4.5 57.2 1.0 C A:ASN77 4.5 61.2 1.0 HA A:PHE76 4.6 66.0 1.0 CG A:LEU282 4.6 50.0 1.0 N A:GLN283 4.6 57.2 1.0 HA A:GLN283 4.6 62.5 1.0 HE1 A:MET78 4.7 77.9 1.0 CA A:ASN77 4.7 59.3 1.0 N A:ALA153 4.7 52.9 1.0 HG2 A:MET78 4.7 73.3 1.0 N A:ASN77 4.7 59.7 1.0 HB3 A:PHE76 4.7 67.8 1.0 HA3 A:GLY278 4.7 61.2 1.0 CA A:ALA153 4.8 53.3 1.0 O A:GLY278 4.8 57.9 1.0 HD11 A:LEU118 4.8 57.9 1.0 CG A:ASN77 4.8 59.4 1.0 CA A:PHE76 4.9 56.6 1.0 HA A:LEU282 4.9 56.8 1.0 H A:LEU282 4.9 58.9 1.0 HE22 A:GLN283 4.9 61.5 1.0 CA A:GLN283 5.0 57.8 1.0 CB A:GLN283 5.0 54.9 1.0

Sodium binding site 7 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:63.2 occ:1.00 HD21 A:ASN499 2.5 61.2 1.0 OD1 A:ASN288 2.7 57.8 1.0 O A:ASP289 2.8 60.0 1.0 HD11 A:LEU541 2.9 64.8 1.0 HD21 A:LEU541 2.9 67.8 1.0 HB2 A:LEU290 3.0 64.4 1.0 HD21 A:ASN288 3.0 63.1 1.0 HD22 A:LEU541 3.1 67.8 1.0 HD2 A:HIS50 3.1 66.6 1.0 C A:ASP289 3.2 58.9 1.0 HB2 A:ASP48 3.2 63.8 1.0 HD13 A:LEU541 3.2 64.8 1.0 CG A:ASN288 3.3 57.7 1.0 ND2 A:ASN499 3.3 53.2 1.0 CD2 A:LEU541 3.4 55.8 1.0 ND2 A:ASN288 3.4 58.4 1.0 H A:ASP289 3.4 61.3 1.0 CD1 A:LEU541 3.4 55.0 1.0 N A:ASP289 3.6 60.9 1.0 HA A:ASP48 3.7 67.0 1.0 HA A:ASP289 3.8 63.2 1.0 CA A:ASP289 3.8 60.7 1.0 CB A:LEU290 3.8 56.5 1.0 N A:LEU290 3.8 54.1 1.0 OD1 A:ASN499 3.9 56.0 1.0 HD22 A:ASN499 3.9 61.2 1.0 CB A:ASP48 4.0 59.8 1.0 HA A:LEU290 4.0 62.5 1.0 CD2 A:HIS50 4.0 57.3 1.0 CG A:ASN499 4.1 54.6 1.0 CG A:LEU541 4.1 55.1 1.0 HB3 A:ASP48 4.1 63.8 1.0 H A:THR49 4.1 60.7 1.0 CA A:LEU290 4.1 55.2 1.0 HB3 A:LEU290 4.1 64.4 1.0 HD22 A:ASN288 4.1 63.1 1.0 HD23 A:LEU541 4.3 67.8 1.0 CA A:ASP48 4.3 61.0 1.0 HD12 A:LEU541 4.3 64.8 1.0 O A:THR49 4.3 51.7 1.0 C A:ASN288 4.4 56.5 1.0 H A:LEU290 4.5 60.2 1.0 HD13 A:LEU290 4.5 60.7 1.0 N A:THR49 4.5 52.0 1.0 HB3 A:HIS50 4.6 62.6 1.0 CB A:ASN288 4.6 57.0 1.0 HG A:LEU541 4.7 65.4 1.0 HA A:ASN288 4.7 60.3 1.0 C A:ASP48 4.7 59.5 1.0 HD22 A:LEU290 4.8 63.3 1.0 CA A:ASN288 4.8 56.9 1.0 HE2 A:HIS50 4.9 64.3 1.0 HB2 A:LEU541 4.9 67.2 1.0 NE2 A:HIS50 4.9 56.5 1.0 CG A:LEU290 4.9 55.1 1.0

Sodium binding site 8 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na610 b:77.0 occ:1.00 HG A:SER362 2.6 73.0 1.0 O A:HOH861 2.6 63.3 1.0 OG A:SER362 2.8 57.8 1.0 OG A:SER360 2.8 60.2 1.0 HB2 A:SER360 3.2 68.7 1.0 HB2 A:SER362 3.3 70.0 1.0 HA A:THR32 3.3 73.1 1.0 C A:THR32 3.3 62.9 1.0 HA A:PHE33 3.4 73.9 1.0 HE1 A:PHE524 3.5 64.7 1.0 HG A:SER360 3.5 78.6 1.0 O A:THR32 3.5 62.9 1.0 CB A:SER360 3.6 55.7 1.0 CB A:SER362 3.6 56.5 1.0 HB A:THR301 3.6 69.0 1.0 N A:PHE33 3.6 65.2 1.0 CA A:THR32 3.8 63.8 1.0 HD1 A:PHE524 3.9 61.9 1.0 O A:VAL31 3.9 64.9 1.0 H A:PHE33 4.0 73.5 1.0 CA A:PHE33 4.0 65.1 1.0 N A:ILE361 4.0 61.3 1.0 N A:SER362 4.1 56.4 1.0 HA A:ILE361 4.1 69.8 1.0 H A:SER362 4.1 68.9 1.0 C A:SER360 4.1 57.0 1.0 H A:ILE361 4.2 68.3 1.0 CE1 A:PHE524 4.2 55.7 1.0 HB3 A:SER360 4.3 68.7 1.0 C A:ILE361 4.3 61.8 1.0 HB3 A:SER362 4.3 70.0 1.0 CA A:ILE361 4.4 62.2 1.0 N A:THR32 4.4 67.0 1.0 C A:VAL31 4.4 64.7 1.0 CD1 A:PHE524 4.4 54.3 1.0 O A:SER360 4.4 55.2 1.0 CA A:SER362 4.5 56.8 1.0 C A:PHE33 4.5 66.4 1.0 CB A:THR301 4.5 55.7 1.0 CA A:SER360 4.5 57.5 1.0 HB2 A:TYR305 4.5 62.1 1.0 HD2 A:TYR305 4.7 60.9 1.0 O A:PHE33 4.7 67.4 1.0 O A:THR301 4.8 55.1 1.0 OG1 A:THR301 4.8 54.6 1.0 O A:ILE361 4.9 61.7 1.0 HB3 A:SER34 4.9 76.4 1.0 HA A:SER362 5.0 69.8 1.0

Sodium binding site 9 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na611 b:65.5 occ:1.00 H A:MET496 2.0 63.8 1.0 HE2 A:PHE51 2.7 67.7 1.0 O A:HOH856 2.8 59.0 1.0 N A:MET496 2.8 55.4 1.0 O A:PRO286 2.9 52.3 1.0 HB2 A:MET496 2.9 62.8 1.0 HA A:ASN495 2.9 64.9 1.0 HE3 A:MET496 3.0 63.7 1.0 HB3 A:ASN495 3.2 64.5 1.0 HE2 A:MET496 3.2 63.7 1.0 CE2 A:PHE51 3.4 54.6 1.0 CE A:MET496 3.5 52.3 1.0 CA A:ASN495 3.5 57.1 1.0 HA A:VAL287 3.6 57.8 1.0 CB A:MET496 3.6 53.5 1.0 HD22 A:ASN495 3.6 66.5 1.0 CA A:MET496 3.6 53.2 1.0 C A:ASN495 3.6 56.9 1.0 O A:MET496 3.7 55.0 1.0 HG3 A:MET496 3.7 61.9 1.0 CB A:ASN495 3.8 57.4 1.0 C A:PRO286 3.8 50.5 1.0 HD2 A:PHE51 4.0 64.8 1.0 CD2 A:PHE51 4.1 53.2 1.0 C A:MET496 4.1 54.3 1.0 CG A:MET496 4.1 52.9 1.0 O A:ASN285 4.1 58.4 1.0 HZ A:PHE51 4.2 69.0 1.0 HE1 A:MET496 4.2 63.7 1.0 ND2 A:ASN495 4.2 57.5 1.0 CZ A:PHE51 4.2 55.0 1.0 NA A:NA604 4.3 63.2 1.0 N A:VAL287 4.4 48.6 1.0 CA A:VAL287 4.4 49.5 1.0 C A:ASN285 4.4 59.3 1.0 HB3 A:MET496 4.4 62.8 1.0 HB3 A:ASN285 4.5 64.1 1.0 CG A:ASN495 4.5 58.1 1.0 HA A:MET496 4.5 59.5 1.0 HB2 A:ASN495 4.6 64.5 1.0 HG22 A:VAL287 4.6 61.7 1.0 H A:ASN288 4.6 57.5 1.0 N A:PRO286 4.7 51.0 1.0 HA A:ASN285 4.7 63.4 1.0 SD A:MET496 4.7 54.1 1.0 O A:ASN495 4.8 57.0 1.0 CA A:PRO286 4.9 51.1 1.0 HD21 A:ASN495 4.9 66.5 1.0 N A:ASN495 4.9 56.6 1.0 O A:ASN494 4.9 59.4 1.0

Sodium binding site 10 out of 47 in the Crystal Structure of Phospholipase D From Moritella Sp. JT01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Phospholipase D From Moritella Sp. JT01 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:64.5 occ:1.00 OG1 B:THR49 2.6 63.7 1.0 O B:VAL287 2.7 57.7 1.0 O B:TYR281 2.8 60.2 1.0 HB2 B:PRO286 2.8 68.1 1.0 HB3 B:TYR281 2.9 67.0 1.0 HA B:TYR281 2.9 72.5 1.0 HB B:THR49 3.0 67.4 1.0 HG1 B:THR49 3.0 65.8 1.0 HD1 B:TYR281 3.0 67.6 1.0 C B:THR49 3.2 62.9 1.0 CB B:THR49 3.2 65.0 1.0 HA B:HIS50 3.2 69.8 1.0 O B:THR49 3.3 63.4 1.0 N B:HIS50 3.4 59.9 1.0 CA B:TYR281 3.5 62.5 1.0 C B:TYR281 3.5 61.9 1.0 CB B:TYR281 3.5 60.0 1.0 HB3 B:PRO286 3.6 68.1 1.0 CB B:PRO286 3.6 58.8 1.0 H B:HIS50 3.7 69.0 1.0 CA B:HIS50 3.8 59.6 1.0 CA B:THR49 3.8 63.1 1.0 CD1 B:TYR281 3.8 60.1 1.0 C B:VAL287 3.8 56.4 1.0 HA B:ASN288 3.9 65.9 1.0 HB1 B:ALA114 4.0 75.4 1.0 CG B:TYR281 4.2 59.6 1.0 HB2 B:ALA114 4.2 75.4 1.0 HD23 B:LEU282 4.2 69.7 1.0 HA B:THR49 4.3 65.8 1.0 HB2 B:TYR281 4.4 67.0 1.0 N B:VAL287 4.4 59.0 1.0 H B:VAL287 4.4 67.6 1.0 HE2 B:HIS274 4.4 67.9 1.0 H B:ASP289 4.4 68.7 1.0 CA B:PRO286 4.5 57.9 1.0 C B:PRO286 4.5 56.9 1.0 CB B:ALA114 4.6 68.1 1.0 HA B:PRO286 4.6 66.3 1.0 CG2 B:THR49 4.6 68.4 1.0 C B:HIS50 4.6 58.8 1.0 CA B:ASN288 4.7 56.5 1.0 N B:ASN288 4.7 55.2 1.0 HG21 B:THR49 4.7 72.4 1.0 CG B:PRO286 4.7 57.5 1.0 CA B:VAL287 4.7 57.9 1.0 N B:TYR281 4.8 59.7 1.0 O B:ASP280 4.8 66.2 1.0 N B:LEU282 4.8 57.9 1.0 HG3 B:PRO286 4.8 64.7 1.0 HG2 B:PRO286 4.9 64.7 1.0 H B:THR49 4.9 68.2 1.0 HB3 B:HIS50 4.9 68.1 1.0 N B:ASP289 4.9 62.2 1.0 N B:THR49 4.9 63.8 1.0 CE1 B:TYR281 5.0 60.3 1.0 HB B:VAL287 5.0 64.5 1.0

Y.H.Wang, X.J.Mao, J.Wang, F.H.Wang. Crystal Structure of Phospholipase D From Moritella Sp. JT01 To Be Published.