Atomistry » Sodium » PDB 5hn3-5i9b » 5hz7
Atomistry »
  Sodium »
    PDB 5hn3-5i9b »
      5hz7 »

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

Go back to Sodium Binding Sites List in 5hz7
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

Go back to Sodium Binding Sites List in 5hz7
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy