Sodium in PDB 7l6j: Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia

Protein crystallography data

The structure of Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia, PDB code: 7l6j was solved by G.Minasov, L.Shuvalova, O.Kiryukhina, I.Dubrovska, G.Wiersum, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.45 / 1.78
Space group I 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 171.693, 171.693, 171.693, 90, 90, 90
R / Rfree (%) 13.7 / 15.4

Other elements in 7l6j:

The structure of Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia (pdb code 7l6j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia, PDB code: 7l6j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 7l6j

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Sodium binding site 1 out of 7 in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia


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 the Putative Hydrolase From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:46.3
occ:1.00
 O A:HOH807 2.3 38.0 1.0
O A:HOH538 2.4 36.1 1.0
O A:HOH597 2.5 40.4 1.0
O A:HOH482 2.8 48.4 1.0
NA A:NA304 2.9 43.7 1.0
N A:SER-2 4.2 51.9 1.0
O A:HOH752 4.3 49.4 1.0
OG A:SER-2 4.3 44.0 1.0
O A:PRO4 4.3 38.2 1.0
O A:HOH735 4.5 37.5 0.5
O A:HOH655 4.7 34.4 1.0
O A:HOH735 4.7 39.3 0.5
CB A:SER-2 4.9 49.0 1.0

Sodium binding site 2 out of 7 in 7l6j

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Sodium binding site 2 out of 7 in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia


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 the Putative Hydrolase From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:27.5
occ:1.00
 O A:HOH648 2.3 31.9 1.0
O A:PHE46 2.3 26.5 1.0
O A:HOH610 2.4 29.6 1.0
O A:HOH655 2.4 34.4 1.0
O A:HOH558 2.4 24.5 1.0
O A:ALA44 2.5 25.1 1.0
NA A:NA304 3.1 43.7 1.0
C A:ALA44 3.5 24.6 1.0
C A:PHE46 3.5 24.9 1.0
O A:HOH734 4.0 50.5 1.0
CA A:ALA44 4.0 23.8 1.0
N A:ALA48 4.1 25.4 1.0
O A:LEU43 4.1 21.0 1.0
O A:HOH793 4.2 48.7 1.0
O A:HOH765 4.3 53.0 1.0
CA A:ASP47 4.3 26.4 1.0
N A:PHE46 4.3 23.1 1.0
N A:ASP47 4.4 25.3 1.0
O A:HOH534 4.5 48.2 1.0
CA A:PHE46 4.5 23.7 1.0
C A:ALA45 4.6 24.1 1.0
N A:ALA45 4.6 23.6 1.0
C A:ASP47 4.7 25.4 1.0
CB A:ALA48 4.7 25.4 1.0
O A:HOH807 4.8 38.0 1.0
O A:HOH746 4.9 43.0 1.0
O A:HOH538 4.9 36.1 1.0
O A:ALA45 5.0 23.6 1.0
C A:LEU43 5.0 21.1 1.0

Sodium binding site 3 out of 7 in 7l6j

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Sodium binding site 3 out of 7 in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia


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 the Putative Hydrolase From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:43.7
occ:1.00
 O A:HOH655 2.2 34.4 1.0
O A:HOH538 2.3 36.1 1.0
O A:HOH807 2.4 38.0 1.0
O A:ALA44 2.5 25.1 1.0
O A:HOH482 2.6 48.4 1.0
O A:HOH648 2.7 31.9 1.0
NA A:NA302 2.9 46.3 1.0
NA A:NA303 3.1 27.5 1.0
C A:ALA44 3.6 24.6 1.0
O A:HOH534 4.0 48.2 1.0
O A:HOH752 4.3 49.4 1.0
O A:PHE46 4.4 26.5 1.0
N A:ALA45 4.5 23.6 1.0
CA A:ALA44 4.5 23.8 1.0
OG A:SER-2 4.5 44.0 1.0
CA A:ALA45 4.5 23.9 1.0
O A:HOH597 4.6 40.4 1.0
C A:ALA45 4.7 24.1 1.0
CB A:ALA44 4.7 25.2 1.0
O A:ALA45 4.8 23.6 1.0
O A:HOH734 4.8 50.5 1.0
O A:HOH765 4.8 53.0 1.0
O A:PRO4 4.8 38.2 1.0
O A:HOH610 4.8 29.6 1.0

Sodium binding site 4 out of 7 in 7l6j

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Sodium binding site 4 out of 7 in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia


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 the Putative Hydrolase From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:20.2
occ:0.50
 O A:HOH784 2.2 25.0 0.3
O A:HOH658 2.3 40.7 1.0
O A:GLU208 2.3 19.5 0.6
O A:GLU208 2.4 19.3 0.4
O A:HOH456 2.5 20.7 0.5
O A:HOH456 3.3 22.8 0.5
C A:GLU208 3.5 19.7 0.4
C A:GLU208 3.5 20.0 0.6
O A:HOH543 3.6 33.2 1.0
OXT A:LEU210 3.8 23.2 1.0
CA A:GLU208 4.2 20.8 0.4
CA A:GLU208 4.3 21.4 0.6
N A:VAL209 4.4 18.0 1.0
CA A:VAL209 4.6 18.8 1.0
O A:HOH466 4.6 21.4 1.0
O A:LEU207 4.6 20.3 1.0
C A:VAL209 4.6 19.3 1.0
O A:HOH740 4.7 30.4 0.3
N A:LEU210 4.9 19.0 1.0
C A:LEU210 5.0 21.5 1.0

Sodium binding site 5 out of 7 in 7l6j

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Sodium binding site 5 out of 7 in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia


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 the Putative Hydrolase From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:23.0
occ:1.00
 OE1 A:GLN27 2.3 21.9 1.0
O A:HOH714 2.4 27.6 1.0
O A:HOH517 2.5 16.6 1.0
O A:HOH613 2.5 30.2 1.0
O A:ARG25 2.6 16.1 1.0
CD A:GLN27 3.2 21.5 1.0
C A:ARG25 3.6 16.4 1.0
CG A:GLN27 3.8 19.4 1.0
N A:ARG25 3.8 16.4 1.0
NH1 A:ARG30 3.9 18.6 1.0
NE2 A:GLN145 4.0 13.9 1.0
CA A:ARG25 4.1 16.7 1.0
CB A:ARG25 4.1 18.3 1.0
NE2 A:GLN27 4.2 21.9 1.0
O A:HOH736 4.4 27.3 1.0
O A:HOH786 4.4 44.8 1.0
O A:HOH438 4.6 18.2 1.0
OE1 A:GLU170 4.7 16.0 1.0
N A:PRO26 4.8 16.2 1.0
O A:HOH632 4.9 39.0 1.0
C A:TRP24 5.0 16.3 1.0

Sodium binding site 6 out of 7 in 7l6j

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Sodium binding site 6 out of 7 in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia


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 the Putative Hydrolase From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:33.5
occ:1.00
 O A:HOH700 2.3 33.3 1.0
O A:HOH804 2.4 41.7 1.0
O A:HOH481 2.5 30.6 1.0
O A:HOH674 2.5 17.1 0.6
O A:SER132 2.5 13.8 1.0
O A:HOH434 2.7 39.6 1.0
O A:HOH674 3.5 12.4 0.4
C A:SER132 3.7 14.6 1.0
O A:HOH620 3.8 13.9 1.0
O A:HOH477 4.0 22.4 1.0
O A:PHE129 4.1 14.4 1.0
N A:SER132 4.1 14.5 1.0
OD1 A:ASN133 4.4 15.0 1.0
O A:HOH531 4.4 35.5 1.0
CL A:CL301 4.5 29.8 0.7
O A:HOH699 4.6 33.7 0.5
CA A:SER132 4.6 14.4 1.0
N A:ASN133 4.6 14.1 1.0
CL A:CL301 4.6 28.8 0.3
O A:HOH683 4.7 23.0 0.5
CA A:ASN133 4.7 14.4 1.0
NH1 A:ARG167 4.7 23.4 0.6
N A:ARG131 4.9 14.3 1.0
C A:ARG131 5.0 14.7 1.0

Sodium binding site 7 out of 7 in 7l6j

Go back to Sodium Binding Sites List in 7l6j
Sodium binding site 7 out of 7 in the Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia


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 the Putative Hydrolase From Stenotrophomonas Maltophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:41.2
occ:1.00
 O A:HOH562 2.5 32.2 1.0
O A:HOH471 2.6 16.6 0.5
O A:HOH666 2.8 37.5 1.0
O A:HOH695 2.8 45.4 1.0
O A:HOH471 3.5 23.9 0.5
NH2 A:ARG143 3.9 17.1 1.0
O A:HOH748 4.2 46.9 1.0
O A:ARG141 4.3 16.6 1.0
O A:HOH487 4.5 25.5 1.0
O A:HOH696 4.7 17.0 0.5
CZ A:ARG143 4.7 16.7 1.0
O A:HOH419 4.7 36.7 1.0
NE A:ARG143 4.8 16.6 1.0
O A:ASP29 5.0 15.8 1.0

Reference:

G.Minasov, L.Shuvalova, O.Kiryukhina, I.Dubrovska, G.Wiersum, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the Putative Hydrolase From Stenotrophomonas Maltophilia To Be Published.
Page generated: Tue Oct 8 17:34:09 2024

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