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Sodium in PDB 5hz7: High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp

Protein crystallography data

The structure of High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp, PDB code: 5hz7 was solved by J.-L.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.05 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.570, 68.440, 109.580, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19.1

Sodium Binding Sites:

The binding sites of Sodium atom in the High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp (pdb code 5hz7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp, PDB code: 5hz7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5hz7

Go back to Sodium Binding Sites List in 5hz7
Sodium binding site 1 out of 5 in the High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:36.9
occ:1.00
 H A:ALA83 1.9 30.2 1.0
O A:HOH1078 2.7 46.9 1.0
N A:ALA83 2.8 25.2 1.0
O A:HOH1197 2.8 54.9 1.0
HB3 A:ALA83 2.8 36.6 1.0
OE1 A:GLU282 2.8 24.2 1.0
HZ2 A:LYS278 3.0 23.0 0.3
HA A:PRO82 3.1 29.7 1.0
HB2 A:ALA83 3.1 36.6 1.0
CB A:ALA83 3.3 30.5 1.0
HB3 A:PHE86 3.3 27.3 1.0
HB2 A:PHE86 3.4 27.3 1.0
CD A:GLU282 3.5 22.2 1.0
OE2 A:GLU282 3.6 22.2 1.0
CA A:ALA83 3.6 28.0 1.0
HE2 A:LYS278 3.7 27.0 0.2
C A:PRO82 3.7 25.4 1.0
HZ1 A:LYS278 3.7 23.0 0.3
CA A:PRO82 3.7 24.8 1.0
NZ A:LYS278 3.7 19.2 0.3
CB A:PHE86 3.8 22.8 1.0
O A:HOH813 3.9 28.7 1.0
HB2 A:PRO82 4.1 30.6 1.0
HE3 A:LYS278 4.1 23.8 0.3
HZ3 A:LYS278 4.2 27.6 0.2
HB1 A:ALA83 4.2 36.6 1.0
CB A:PRO82 4.3 25.5 1.0
HA A:ALA83 4.3 33.6 1.0
HB3 A:PRO82 4.4 30.6 1.0
HZ3 A:LYS278 4.4 23.0 0.3
CG A:PHE86 4.5 21.4 1.0
O A:ALA83 4.5 27.8 1.0
CE A:LYS278 4.5 19.9 0.3
CE A:LYS278 4.5 22.5 0.2
C A:ALA83 4.5 28.4 1.0
H A:PHE86 4.5 29.9 1.0
HE3 A:LYS278 4.7 27.0 0.2
NZ A:LYS278 4.7 23.0 0.2
HE2 A:LYS278 4.8 23.8 0.3
HZ1 A:LYS278 4.8 27.6 0.2
O A:THR81 4.8 25.3 1.0
O A:HOH804 4.9 48.4 1.0
HD2 A:PHE86 4.9 25.5 1.0
O A:PRO82 4.9 26.3 1.0
CG A:GLU282 5.0 20.5 1.0
CD2 A:PHE86 5.0 21.3 1.0

Sodium binding site 2 out of 5 in 5hz7

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Sodium binding site 2 out of 5 in the High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:31.1
occ:1.00
 H A:LEU104 2.1 21.9 1.0
OE2 A:GLU79 2.7 24.6 1.0
O A:ILE80 2.8 21.8 1.0
O A:HOH1252 2.8 30.7 1.0
N A:LEU104 2.9 18.2 1.0
HB2 A:LEU104 3.0 20.8 1.0
HG3 A:GLU79 3.0 26.4 1.0
HA A:LYS103 3.1 26.1 1.0
HG2 A:GLU79 3.1 26.4 1.0
HG A:LEU104 3.2 20.9 1.0
CG A:GLU79 3.4 22.0 1.0
CD A:GLU79 3.5 24.5 1.0
HG22 A:THR81 3.5 32.5 1.0
CB A:LEU104 3.6 17.3 1.0
HB3 A:LYS103 3.7 29.3 1.0
HD12 A:LEU104 3.7 23.9 1.0
CA A:LEU104 3.7 17.5 1.0
CA A:LYS103 3.8 21.8 1.0
CG A:LEU104 3.8 17.5 1.0
C A:LYS103 3.8 19.3 1.0
O A:LEU104 3.9 18.7 1.0
C A:ILE80 4.0 22.5 1.0
HG23 A:THR81 4.0 32.5 1.0
HA A:THR81 4.0 29.0 1.0
H A:ILE80 4.1 23.7 1.0
CB A:LYS103 4.2 24.4 1.0
CG2 A:THR81 4.2 27.1 1.0
CD1 A:LEU104 4.2 19.9 1.0
HG2 A:LYS103 4.3 34.0 1.0
O A:HOH645 4.3 52.4 1.0
C A:LEU104 4.3 18.3 1.0
O A:HOH1232 4.4 46.6 1.0
HB3 A:LEU104 4.5 20.8 1.0
N A:ILE80 4.5 19.8 1.0
O A:HOH808 4.6 27.3 1.0
HA A:LEU104 4.6 21.0 1.0
OE1 A:GLU79 4.7 25.9 1.0
HD11 A:LEU104 4.7 23.9 1.0
CA A:THR81 4.8 24.1 1.0
N A:THR81 4.8 22.1 1.0
CG A:LYS103 4.8 28.3 1.0
O A:GLY102 4.8 26.6 1.0
HD2 A:PRO82 4.8 31.1 1.0
CA A:ILE80 4.9 21.9 1.0
HG21 A:THR81 4.9 32.5 1.0
CB A:GLU79 4.9 21.0 1.0
HB A:ILE80 4.9 25.2 1.0
O A:HOH989 4.9 40.9 1.0
O A:HOH1000 5.0 39.5 1.0
HD13 A:LEU104 5.0 23.9 1.0

Sodium binding site 3 out of 5 in 5hz7

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Sodium binding site 3 out of 5 in the High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:29.4
occ:1.00
 H A:GLY301 2.3 24.5 1.0
HD11 A:ILE318 2.5 27.9 1.0
OD1 A:ASN295 2.7 19.9 1.0
O A:GLY301 2.8 20.4 1.0
O A:HOH948 2.9 25.9 1.0
H A:LEU300 3.0 20.9 1.0
N A:GLY301 3.0 20.4 1.0
HB3 A:PRO299 3.1 23.2 1.0
HD13 A:LEU312 3.1 25.0 1.0
HD21 A:ASN295 3.4 22.6 1.0
CD1 A:ILE318 3.4 23.2 1.0
N A:LEU300 3.4 17.4 1.0
HD12 A:ILE318 3.5 27.9 1.0
HA2 A:GLY301 3.5 26.3 1.0
C A:GLY301 3.6 21.1 1.0
CA A:GLY301 3.6 21.9 1.0
CG A:ASN295 3.6 18.6 1.0
HA A:PRO299 3.7 22.3 1.0
HD22 A:LEU312 3.7 26.4 1.0
HB2 A:LEU300 3.8 21.9 1.0
CB A:PRO299 3.8 19.3 1.0
ND2 A:ASN295 3.8 18.9 1.0
CD1 A:LEU312 4.0 20.8 1.0
HD13 A:ILE318 4.0 27.9 1.0
HZ3 A:TRP233 4.0 22.1 1.0
C A:LEU300 4.0 19.8 1.0
C A:PRO299 4.0 18.4 1.0
CA A:PRO299 4.0 18.6 1.0
HB2 A:PRO299 4.0 23.2 1.0
HG13 A:ILE318 4.1 24.9 1.0
HD11 A:LEU312 4.1 25.0 1.0
CA A:LEU300 4.2 17.2 1.0
CG1 A:ILE318 4.3 20.7 1.0
HB3 A:LEU312 4.4 24.8 1.0
CB A:LEU300 4.5 18.2 1.0
CD2 A:LEU312 4.5 22.0 1.0
HB3 A:PRO230 4.5 22.5 1.0
HA3 A:GLY301 4.5 26.3 1.0
HD12 A:LEU312 4.6 25.0 1.0
HG12 A:ILE318 4.6 24.9 1.0
HD21 A:LEU312 4.6 26.4 1.0
HD22 A:ASN295 4.7 22.6 1.0
CG A:LEU312 4.7 20.2 1.0
HG13 A:VAL303 4.7 24.2 1.0
CZ3 A:TRP233 4.7 18.4 1.0
N A:ALA302 4.8 21.6 1.0
HB2 A:PRO230 5.0 22.5 1.0
O A:PRO299 5.0 18.8 1.0
CB A:ASN295 5.0 18.7 1.0

Sodium binding site 4 out of 5 in 5hz7

Go back to Sodium Binding Sites List in 5hz7
Sodium binding site 4 out of 5 in the High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:32.8
occ:1.00
 H A:TYR177 2.4 27.9 1.0
O A:HOH770 2.8 41.5 1.0
HD2 A:TYR177 2.8 27.3 1.0
HA A:LYS176 2.9 30.7 1.0
HB2 A:LYS176 3.0 34.6 1.0
O A:HOH767 3.1 27.6 1.0
N A:TYR177 3.2 23.3 1.0
HG21 A:ILE334 3.5 23.7 1.0
CA A:LYS176 3.5 25.6 1.0
HB2 A:TYR177 3.5 26.9 1.0
CB A:LYS176 3.6 28.8 1.0
CD2 A:TYR177 3.6 22.8 1.0
O A:HOH1059 3.8 41.3 1.0
C A:LYS176 3.9 23.7 1.0
HB3 A:LYS176 3.9 34.6 1.0
HG22 A:ILE334 3.9 23.7 1.0
CG2 A:ILE334 4.0 19.8 1.0
CB A:TYR177 4.1 22.5 1.0
HG23 A:ILE334 4.2 23.7 1.0
O A:HOH737 4.2 32.7 1.0
CA A:TYR177 4.2 23.4 1.0
CG A:TYR177 4.3 22.4 1.0
HE2 A:TYR172 4.3 32.4 1.0
HE2 A:TYR177 4.5 28.5 1.0
CE2 A:TYR177 4.5 23.7 1.0
O A:TYR177 4.6 25.5 1.0
O A:GLY175 4.7 28.7 1.0
O A:HOH793 4.8 42.2 1.0
N A:LYS176 4.8 26.8 1.0
HD2 A:TYR172 4.9 31.3 1.0
C A:TYR177 4.9 24.2 1.0
CG A:LYS176 4.9 31.1 1.0
HD13 A:ILE334 5.0 27.2 1.0
HA A:TYR177 5.0 28.0 1.0

Sodium binding site 5 out of 5 in 5hz7

Go back to Sodium Binding Sites List in 5hz7
Sodium binding site 5 out of 5 in the High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High-Resolution Crystal Structure of the Minor Dna-Binding Pilin Comp From Neisseria Meningitidis in Fusion with Mbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:58.8
occ:1.00
 O A:HOH1229 2.3 52.5 1.0
O A:HOH898 2.5 41.4 1.0
O A:HOH1195 2.7 50.8 1.0
O A:ALA319 2.7 19.9 1.0
HB2 A:GLU323 3.0 29.1 1.0
HB2 A:MET322 3.2 27.4 0.6
HB1 A:ALA319 3.3 25.5 1.0
HE3 A:MET322 3.4 35.3 0.6
H A:GLU323 3.4 25.1 1.0
HA A:ALA319 3.5 24.5 1.0
C A:ALA319 3.5 19.2 1.0
N A:GLU323 3.7 20.9 1.0
HB2 A:MET322 3.7 28.5 0.4
HA A:GLU323 3.8 25.8 1.0
CB A:GLU323 3.8 24.2 1.0
CA A:ALA319 3.9 20.4 1.0
CA A:GLU323 4.0 21.5 1.0
CB A:MET322 4.0 22.8 0.6
HB3 A:MET322 4.0 27.4 0.6
CB A:ALA319 4.1 21.2 1.0
C A:MET322 4.2 21.1 0.4
CE A:MET322 4.3 29.4 0.6
C A:MET322 4.3 19.7 0.6
HB3 A:MET322 4.3 28.5 0.4
HE1 A:MET322 4.4 35.3 0.6
O A:HOH1069 4.4 52.8 1.0
CB A:MET322 4.4 23.8 0.4
HB3 A:GLU323 4.5 29.1 1.0
HG3 A:GLU323 4.5 34.5 1.0
HB2 A:ALA319 4.6 25.5 1.0
HA A:ALA320 4.7 22.8 1.0
N A:ALA320 4.7 19.1 1.0
CG A:GLU323 4.7 28.7 1.0
CA A:MET322 4.7 19.9 0.6
HE2 A:MET322 4.7 35.3 0.6
OE1 A:GLN326 4.7 30.8 1.0
HB3 A:ALA319 4.7 25.5 1.0
H A:MET322 4.8 23.6 0.4
CA A:MET322 4.8 21.4 0.4
OE1 A:GLU323 4.8 35.2 1.0
H A:MET322 4.8 22.3 0.6
O A:MET322 4.8 21.9 0.4
HE22 A:GLN326 4.9 37.3 1.0
O A:HOH759 4.9 36.5 1.0

Reference:

J.L.Berry, Y.Xu, P.N.Ward, S.M.Lea, S.J.Matthews, V.Pelicic. A Comparative Structure/Function Analysis of Two Type IV Pilin Dna Receptors Defines A Novel Mode of Dna Binding. Structure V. 24 926 2016.
ISSN: ISSN 0969-2126
PubMed: 27161979
DOI: 10.1016/J.STR.2016.04.001
Page generated: Mon Oct 7 21:30:02 2024

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