Sodium in PDB 4x1z: Crystal Structure of Rhdvb P Domain in Complex with H Type 2

The structure of Crystal Structure of Rhdvb P Domain in Complex with H Type 2, PDB code: 4x1z was solved by M.M.Leuthold, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.170, 76.210, 107.680, 90.00, 90.00, 90.00
R / Rfree (%)	10.8 / 13.2

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2 (pdb code 4x1z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2, PDB code: 4x1z:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:18.0 occ:1.00 HH21 B:ARG468 2.4 13.9 1.0 H A:ALA294 2.5 12.7 1.0 HB3 A:ALA293 2.9 14.7 1.0 HB1 A:ALA293 2.9 14.7 1.0 O B:HOH826 3.0 13.8 1.0 O A:HOH864 3.2 21.1 1.0 NH2 B:ARG468 3.2 11.6 1.0 HB3 A:ALA294 3.3 13.3 1.0 N A:ALA294 3.3 10.5 1.0 CB A:ALA293 3.3 12.2 1.0 NH1 A:ARG291 3.3 25.9 0.3 O A:ALA294 3.4 13.2 1.0 HH22 B:ARG468 3.6 13.9 1.0 HE B:ARG468 3.7 12.4 1.0 O A:HOH1062 3.7 39.5 1.0 O A:HOH852 3.7 16.6 1.0 NH2 A:ARG291 3.9 26.7 0.6 HB2 A:ALA293 4.0 14.7 1.0 CA A:ALA294 4.0 9.9 1.0 CB A:ALA294 4.0 11.1 1.0 CZ A:ARG291 4.1 25.7 0.3 C A:ALA294 4.1 10.8 1.0 CZ B:ARG468 4.2 10.5 1.0 NE B:ARG468 4.3 10.3 1.0 C A:ALA293 4.3 10.5 1.0 CA A:ALA293 4.4 10.1 1.0 HB2 A:ALA294 4.4 13.3 1.0 HB1 A:ALA294 4.8 13.3 1.0 O B:HOH1073 4.8 30.2 1.0 HA A:ALA294 4.9 11.9 1.0 HG2 B:GLU476 4.9 26.6 1.0

Sodium binding site 2 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:12.2 occ:1.00 H A:TYR436 2.5 12.1 1.0 HA A:THR435 2.9 12.9 1.0 HD2 A:TYR436 3.0 11.3 1.0 O A:HOH892 3.1 19.8 1.0 HB A:THR435 3.1 13.9 1.0 O A:HOH881 3.1 20.1 1.0 O A:HOH818 3.2 15.5 1.0 HG22 A:THR435 3.3 15.6 1.0 N A:TYR436 3.3 10.1 1.0 CA A:THR435 3.6 10.7 1.0 HB3 A:TYR436 3.6 11.2 1.0 CB A:THR435 3.6 11.6 1.0 CD2 A:TYR436 3.8 9.4 1.0 CG2 A:THR435 3.9 13.0 1.0 C A:THR435 3.9 10.3 1.0 CB A:TYR436 4.2 9.3 1.0 HE22 A:GLN439 4.3 13.3 1.0 CA A:TYR436 4.3 9.2 1.0 HG21 A:THR435 4.3 15.6 1.0 O A:HOH966 4.4 27.6 1.0 CG A:TYR436 4.5 8.9 1.0 O A:HOH989 4.6 29.2 1.0 HG23 A:THR435 4.7 15.6 1.0 O A:HOH1065 4.7 28.4 1.0 HE2 A:TYR436 4.7 12.2 1.0 CE2 A:TYR436 4.8 10.2 1.0 HE21 A:GLN439 4.8 13.3 1.0 HA A:TYR436 4.8 11.0 1.0 O A:HOH823 4.8 14.5 1.0 NE2 A:GLN439 4.8 11.1 1.0 OE1 A:GLN265 4.9 11.1 1.0 N A:THR435 4.9 11.2 1.0 OG1 A:THR435 5.0 11.8 1.0

Sodium binding site 3 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:12.1 occ:1.00 HG22 A:VAL247 2.9 12.6 1.0 O A:HOH776 3.0 9.8 1.0 HB2 A:PRO246 3.0 13.7 1.0 HA A:VAL247 3.1 10.9 1.0 O A:HOH784 3.1 16.6 1.0 O A:HOH783 3.1 16.2 1.0 HG2 A:PRO493 3.2 9.7 1.0 HG12 A:VAL251 3.2 12.8 1.0 HB A:VAL251 3.3 12.2 1.0 HG2 A:PRO246 3.4 15.1 1.0 HG11 A:VAL251 3.5 12.8 1.0 HG23 A:VAL247 3.6 12.6 1.0 CG2 A:VAL247 3.6 10.5 1.0 CG1 A:VAL251 3.7 10.6 1.0 HG3 A:PRO493 3.7 9.7 1.0 N A:VAL247 3.8 9.4 1.0 CA A:VAL247 3.8 9.1 1.0 CG A:PRO493 3.8 8.0 1.0 HA2 A:GLY252 3.9 10.1 1.0 HB3 A:PRO493 3.9 10.6 1.0 CB A:PRO246 3.9 11.4 1.0 C A:PRO246 3.9 9.4 1.0 H A:GLY252 4.0 10.5 1.0 CB A:VAL251 4.0 10.2 1.0 N A:GLY252 4.0 8.8 1.0 H A:VAL247 4.1 11.3 1.0 CG A:PRO246 4.1 12.6 1.0 O A:PRO246 4.1 9.8 1.0 HA3 A:GLY252 4.2 10.1 1.0 CB A:PRO493 4.2 8.8 1.0 CA A:GLY252 4.3 8.4 1.0 CB A:VAL247 4.3 9.8 1.0 HG21 A:VAL247 4.4 12.6 1.0 HB2 A:PRO493 4.4 10.6 1.0 HG3 A:PRO246 4.5 15.1 1.0 C A:VAL251 4.5 8.6 1.0 HG13 A:VAL247 4.5 11.5 1.0 CA A:PRO246 4.5 10.3 1.0 HB3 A:PRO246 4.6 13.7 1.0 HG13 A:VAL251 4.6 12.8 1.0 O A:HOH775 4.7 9.9 1.0 O A:HOH779 4.8 10.1 1.0 O A:HOH998 4.9 33.5 1.0 CA A:VAL251 4.9 9.5 1.0 HG21 A:VAL251 4.9 13.9 1.0

Sodium binding site 4 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:14.7 occ:1.00 H A:PHE344 2.6 13.9 1.0 HZ1 A:LYS402 2.6 20.9 1.0 HG2 A:PRO388 3.0 22.1 1.0 HE2 A:PHE341 3.0 16.7 1.0 HA A:PRO343 3.0 15.8 1.0 HB3 A:PRO343 3.0 17.0 1.0 HZ3 A:LYS402 3.1 20.9 1.0 O A:HOH900 3.2 22.1 1.0 NZ A:LYS402 3.3 17.5 1.0 O A:HOH1038 3.3 32.4 1.0 O A:HOH748 3.3 29.2 1.0 O A:PHE344 3.4 17.9 1.0 N A:PHE344 3.4 11.6 1.0 CA A:PRO343 3.6 13.2 1.0 CB A:PRO343 3.7 14.2 1.0 HD2 A:PRO388 3.8 22.5 1.0 HZ2 A:LYS402 3.8 20.9 1.0 HD3 A:LYS402 3.8 16.3 1.0 CG A:PRO388 3.9 18.4 1.0 CE2 A:PHE341 3.9 13.9 1.0 HD2 A:LYS402 3.9 16.3 1.0 C A:PRO343 4.0 12.0 1.0 HG3 A:PRO388 4.1 22.1 1.0 C A:PHE344 4.2 15.2 1.0 CD A:LYS402 4.2 13.6 1.0 HZ A:PHE341 4.2 17.3 1.0 HB2 A:PRO343 4.2 17.0 1.0 CE A:LYS402 4.3 15.7 1.0 CD A:PRO388 4.3 18.8 1.0 CA A:PHE344 4.4 12.2 1.0 CZ A:PHE341 4.5 14.4 1.0 O A:PRO388 4.6 18.4 1.0 HG3 A:PRO343 4.7 17.7 1.0 HE2 A:LYS402 4.7 18.8 1.0 HB2 A:PRO388 4.8 22.1 1.0 CG A:PRO343 4.8 14.8 1.0 HD2 A:PHE341 4.9 15.5 1.0 CD2 A:PHE341 4.9 12.9 1.0 HD1 A:PHE344 4.9 13.4 1.0 CB A:PRO388 4.9 18.4 1.0 O A:HOH1101 4.9 35.5 1.0 N A:PRO343 5.0 11.6 1.0 CD1 A:PHE344 5.0 11.2 1.0

Sodium binding site 5 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:17.5 occ:1.00 HG1 A:THR394 2.3 14.9 1.0 OG1 A:THR394 3.0 12.4 1.0 O A:HOH987 3.1 30.6 1.0 HD2 A:PRO447 3.1 16.9 1.0 HA A:SER395 3.2 20.8 1.0 HG12 A:ILE331 3.3 18.8 1.0 HD3 A:PRO447 3.3 16.9 1.0 HG2 A:PRO447 3.4 19.4 1.0 CD A:PRO447 3.5 14.1 1.0 HD11 A:ILE331 3.6 19.3 1.0 HB A:THR394 3.6 14.3 1.0 N A:SER395 3.7 15.3 1.0 HB2 A:SER395 3.7 23.4 1.0 C A:THR394 3.8 13.6 1.0 CB A:THR394 3.8 11.9 1.0 CA A:SER395 3.8 17.3 1.0 CG A:PRO447 3.9 16.1 1.0 H A:SER395 4.0 18.4 1.0 O A:THR394 4.0 14.3 1.0 HD13 A:ILE331 4.0 19.3 1.0 CG1 A:ILE331 4.1 15.7 1.0 CD1 A:ILE331 4.1 16.1 1.0 HG3 A:PRO447 4.2 19.4 1.0 CB A:SER395 4.3 19.5 1.0 HG13 A:ILE331 4.4 18.8 1.0 CA A:THR394 4.5 12.7 1.0 HA A:ALA446 4.6 11.8 1.0 HB1 A:ALA446 4.7 13.1 1.0 HG23 A:ILE331 4.7 18.7 1.0 OG A:SER395 4.8 21.5 1.0 N A:PRO447 4.9 12.0 1.0 O A:HOH751 5.0 29.9 1.0

Sodium binding site 6 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:23.1 occ:1.00 HD22 A:ASN281 2.4 28.2 1.0 HD21 A:ASN279 2.5 14.6 1.0 HB3 A:ASN281 3.0 20.6 1.0 O A:HOH753 3.2 17.8 1.0 ND2 A:ASN279 3.3 12.2 1.0 ND2 A:ASN281 3.3 23.5 1.0 HD22 A:ASN279 3.6 14.6 1.0 CB A:ASN281 3.8 17.2 1.0 HD21 A:ASN281 3.8 28.2 1.0 CG A:ASN281 4.0 20.9 1.0 OG A:SER283 4.1 20.1 0.6 HB2 A:ASN281 4.1 20.6 1.0 CB A:SER283 4.2 17.3 1.0 CG A:ASN279 4.2 10.8 1.0 OD1 A:ASN279 4.4 11.6 1.0 O A:HOH828 4.6 16.0 1.0 O A:ASN281 4.7 17.5 1.0 HE2 A:PHE285 4.9 16.6 1.0 O A:HOH724 5.0 11.7 1.0

Sodium binding site 7 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:20.3 occ:1.00 H A:ALA408 2.2 17.2 1.0 O B:HOH1106 2.6 23.2 1.0 O A:VAL373 2.7 10.9 1.0 O A:HOH1109 2.9 22.8 1.0 HA A:VAL407 3.0 16.1 1.0 N A:ALA408 3.0 14.4 1.0 HB2 A:ALA408 3.3 18.9 1.0 O A:THR371 3.3 13.6 1.0 HB A:VAL407 3.3 16.1 1.0 HG2 A:GLN374 3.4 12.8 1.0 HB3 A:ALA408 3.5 18.9 1.0 CA A:VAL407 3.6 13.4 1.0 NA B:NA607 3.7 19.7 1.0 H A:VAL373 3.7 12.6 1.0 CB A:ALA408 3.7 15.8 1.0 HE21 B:GLN374 3.7 14.2 1.0 C A:THR371 3.8 12.6 1.0 N A:VAL373 3.8 10.5 1.0 C A:VAL373 3.8 10.2 1.0 C A:VAL407 3.8 13.5 1.0 CB A:VAL407 3.9 13.4 1.0 CA A:ALA408 3.9 15.5 1.0 HG12 A:VAL407 4.0 15.4 1.0 HA A:THR371 4.0 15.7 1.0 HA A:THR372 4.0 13.5 1.0 HB A:VAL373 4.1 13.1 1.0 C A:THR372 4.1 10.9 1.0 HB2 B:ALA408 4.2 17.8 1.0 NE2 B:GLN374 4.2 11.8 1.0 N A:THR372 4.2 11.6 1.0 CA A:VAL373 4.3 10.5 1.0 CG A:GLN374 4.3 10.7 1.0 HE22 B:GLN374 4.3 14.2 1.0 CA A:THR372 4.3 11.3 1.0 HE21 A:GLN374 4.4 13.8 1.0 HA A:ALA408 4.4 18.6 1.0 CG1 A:VAL407 4.5 12.8 1.0 CA A:THR371 4.5 13.1 1.0 H A:THR409 4.6 19.0 1.0 HG2 B:GLN374 4.6 12.1 1.0 O A:VAL370 4.6 14.1 1.0 HG3 A:GLN374 4.6 12.8 1.0 HB1 A:ALA408 4.6 18.9 1.0 O B:VAL373 4.7 11.2 1.0 H B:ALA408 4.7 17.2 1.0 CB A:VAL373 4.7 10.9 1.0 O A:THR372 4.8 11.6 1.0 HB2 A:GLN374 4.8 12.6 1.0 O A:GLY406 4.8 14.4 1.0 H A:THR372 4.8 13.9 1.0 N A:GLN374 4.9 9.7 1.0 N A:VAL407 4.9 13.1 1.0 NE2 A:GLN374 5.0 11.5 1.0 O A:VAL407 5.0 14.5 1.0 HG11 A:VAL407 5.0 15.4 1.0

Sodium binding site 8 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:12.3 occ:1.00 H B:TYR436 2.5 12.2 1.0 HA B:THR435 3.0 13.0 1.0 HD2 B:TYR436 3.0 11.6 1.0 O B:HOH883 3.1 20.2 1.0 HB B:THR435 3.1 14.4 1.0 O B:HOH890 3.1 19.0 1.0 O B:HOH782 3.1 15.6 1.0 N B:TYR436 3.3 10.2 1.0 HG22 B:THR435 3.3 16.0 1.0 HB3 B:TYR436 3.6 11.3 1.0 CA B:THR435 3.6 10.8 1.0 CB B:THR435 3.7 12.0 1.0 CD2 B:TYR436 3.8 9.7 1.0 CG2 B:THR435 3.9 13.3 1.0 C B:THR435 3.9 10.2 1.0 CB B:TYR436 4.2 9.4 1.0 HE22 B:GLN439 4.3 12.9 1.0 O B:HOH1071 4.3 26.8 1.0 CA B:TYR436 4.3 9.6 1.0 HG21 B:THR435 4.4 16.0 1.0 CG B:TYR436 4.5 9.3 1.0 O B:HOH989 4.6 29.7 1.0 HG23 B:THR435 4.7 16.0 1.0 HE2 B:TYR436 4.7 12.2 1.0 O B:HOH1077 4.8 28.0 1.0 CE2 B:TYR436 4.8 10.2 1.0 HE21 B:GLN439 4.8 12.9 1.0 HA B:TYR436 4.8 11.5 1.0 NE2 B:GLN439 4.8 10.7 1.0 O B:HOH828 4.8 14.7 1.0 OE1 B:GLN265 4.9 11.1 1.0 N B:THR435 4.9 11.1 1.0

Sodium binding site 9 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:11.9 occ:1.00 HG22 B:VAL247 2.9 13.2 1.0 O B:HOH774 3.0 9.5 1.0 HB2 B:PRO246 3.0 13.3 1.0 HA B:VAL247 3.0 10.8 1.0 O B:HOH778 3.1 16.3 1.0 O B:HOH779 3.1 15.6 1.0 HG2 B:PRO493 3.2 9.8 1.0 HG12 B:VAL251 3.2 12.9 1.0 HB B:VAL251 3.3 12.4 1.0 HG2 B:PRO246 3.4 14.8 1.0 HG11 B:VAL251 3.5 12.9 1.0 HG23 B:VAL247 3.6 13.2 1.0 CG2 B:VAL247 3.6 11.0 1.0 CG1 B:VAL251 3.7 10.7 1.0 HG3 B:PRO493 3.7 9.8 1.0 N B:VAL247 3.8 9.2 1.0 CA B:VAL247 3.8 9.0 1.0 CG B:PRO493 3.8 8.2 1.0 HA2 B:GLY252 3.8 10.1 1.0 CB B:PRO246 3.9 11.1 1.0 HB3 B:PRO493 3.9 10.5 1.0 C B:PRO246 3.9 9.4 1.0 H B:GLY252 4.0 10.3 1.0 CB B:VAL251 4.0 10.4 1.0 N B:GLY252 4.0 8.6 1.0 H B:VAL247 4.1 11.1 1.0 CG B:PRO246 4.1 12.4 1.0 O B:PRO246 4.1 9.9 1.0 HA3 B:GLY252 4.2 10.1 1.0 CB B:PRO493 4.2 8.8 1.0 CA B:GLY252 4.2 8.4 1.0 CB B:VAL247 4.3 9.9 1.0 HB2 B:PRO493 4.4 10.5 1.0 HG21 B:VAL247 4.4 13.2 1.0 HG3 B:PRO246 4.5 14.8 1.0 C B:VAL251 4.5 8.1 1.0 HG13 B:VAL247 4.5 11.0 1.0 CA B:PRO246 4.5 10.0 1.0 HB3 B:PRO246 4.6 13.3 1.0 HG13 B:VAL251 4.6 12.9 1.0 O B:HOH773 4.7 9.9 1.0 O B:HOH776 4.8 10.2 1.0 CA B:VAL251 4.9 9.3 1.0 HG21 B:VAL251 4.9 13.8 1.0 O B:HOH988 5.0 30.6 1.0

Sodium binding site 10 out of 14 in the Crystal Structure of Rhdvb P Domain in Complex with H Type 2


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 Rhdvb P Domain in Complex with H Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:17.4 occ:1.00 HG1 B:THR394 3.0 15.0 1.0 OG1 B:THR394 3.0 12.5 1.0 O B:HOH736 3.1 41.9 1.0 HD2 B:PRO447 3.1 16.3 1.0 O B:HOH981 3.1 29.5 1.0 HA B:SER395 3.2 21.3 1.0 HG12 B:ILE331 3.3 18.1 1.0 HD3 B:PRO447 3.3 16.3 1.0 HG2 B:PRO447 3.4 18.6 1.0 CD B:PRO447 3.5 13.6 1.0 HD11 B:ILE331 3.6 19.2 1.0 HB B:THR394 3.6 14.2 1.0 N B:SER395 3.7 15.7 1.0 HB2 B:SER395 3.8 23.6 1.0 CB B:THR394 3.8 11.8 1.0 C B:THR394 3.8 13.7 1.0 CA B:SER395 3.8 17.7 1.0 CG B:PRO447 3.9 15.5 1.0 H B:SER395 4.0 18.9 1.0 O B:THR394 4.0 14.4 1.0 HD13 B:ILE331 4.0 19.2 1.0 CG1 B:ILE331 4.1 15.1 1.0 CD1 B:ILE331 4.1 16.0 1.0 HG3 B:PRO447 4.3 18.6 1.0 CB B:SER395 4.3 19.7 1.0 HG13 B:ILE331 4.4 18.1 1.0 CA B:THR394 4.5 12.8 1.0 O B:HOH1096 4.5 40.5 1.0 HA B:ALA446 4.5 12.1 1.0 HB1 B:ALA446 4.7 13.1 1.0 HG23 B:ILE331 4.7 18.7 1.0 OG B:SER395 4.8 22.0 1.0 O B:HOH749 5.0 30.9 1.0 N B:PRO447 5.0 11.7 1.0

M.M.Leuthold, K.P.Dalton, G.S.Hansman. Structural Analysis of A Rabbit Hemorrhagic Disease Virus Binding to Histo-Blood Group Antigens. J.Virol. V. 89 2378 2015.
ISSN: ESSN 1098-5514
PubMed: 25505081
DOI: 10.1128/JVI.02832-14