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Chlorine in PDB 5vmt: Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad

Protein crystallography data

The structure of Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad, PDB code: 5vmt was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.49 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.450, 132.100, 156.000, 90.00, 94.56, 90.00
R / Rfree (%) 16.5 / 21.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad (pdb code 5vmt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad, PDB code: 5vmt:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5vmt

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Chlorine binding site 1 out of 6 in the Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:39.1
occ:1.00
 NZ A:LYS308 3.2 29.4 1.0
C B:GLY230 3.7 33.6 1.0
CA B:GLY230 3.7 31.0 1.0
CE A:LYS308 3.7 30.2 1.0
O A:HOH545 3.7 55.0 1.0
CB A:ARG297 3.8 40.2 1.0
CD A:LYS308 3.8 37.1 1.0
CB B:SER231 3.8 26.4 1.0
CG A:ARG297 3.9 37.2 1.0
O B:GLY230 3.9 27.9 1.0
N B:SER231 4.0 28.0 1.0
N B:GLY230 4.3 32.1 1.0
CD2 B:LEU173 4.4 30.6 1.0
CD A:ARG297 4.5 37.0 1.0
CA B:SER231 4.6 24.8 1.0
O B:MET174 4.6 26.2 1.0
O A:HOH522 4.7 38.8 1.0
CB A:LYS308 4.7 32.8 1.0
OG B:SER231 4.9 47.7 1.0
CG A:LYS308 4.9 39.1 1.0
O A:HOH535 5.0 27.0 1.0

Chlorine binding site 2 out of 6 in 5vmt

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Chlorine binding site 2 out of 6 in the Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:59.4
occ:1.00
 O B:HOH601 3.5 49.7 1.0
NZ B:LYS308 3.5 40.9 1.0
CB B:ARG297 3.7 46.9 1.0
CD B:LYS308 3.7 36.7 1.0
C A:GLY230 3.7 34.8 1.0
CG B:ARG297 3.7 49.4 1.0
CB A:SER231 3.8 38.8 1.0
CA A:GLY230 3.8 31.1 1.0
CE B:LYS308 3.9 40.9 1.0
O A:GLY230 4.0 28.6 1.0
N A:SER231 4.0 34.5 1.0
CD B:ARG297 4.2 50.9 1.0
N A:GLY230 4.4 32.9 1.0
CA A:SER231 4.6 32.6 1.0
CD2 A:LEU173 4.6 36.3 1.0
O A:MET174 4.7 30.4 1.0
O B:HOH525 4.7 48.4 1.0
CB B:LYS308 4.7 33.0 1.0
CG B:LYS308 4.8 34.1 1.0
OG A:SER231 4.8 50.2 1.0
NE B:ARG297 4.8 55.1 1.0
O B:HOH583 4.9 33.3 1.0
O B:GLN295 5.0 36.2 1.0

Chlorine binding site 3 out of 6 in 5vmt

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Chlorine binding site 3 out of 6 in the Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:56.4
occ:1.00
 O C:HOH546 2.9 35.2 1.0
CE C:LYS308 3.2 49.7 1.0
NZ C:LYS308 3.3 47.0 1.0
O C:HOH556 3.4 52.3 1.0
CB C:ARG297 3.7 47.2 1.0
CA D:GLY230 3.8 37.9 1.0
OG D:SER231 3.8 59.1 1.0
CG C:ARG297 3.8 49.1 1.0
C D:GLY230 3.8 38.7 1.0
N D:SER231 4.1 36.5 1.0
CB D:SER231 4.1 45.9 1.0
O D:GLY230 4.3 41.5 1.0
CD C:LYS308 4.4 46.0 1.0
N D:GLY230 4.4 44.5 1.0
CD C:ARG297 4.4 49.8 1.0
CD2 D:LEU173 4.5 58.1 1.0
CB C:LYS308 4.5 37.1 1.0
CG C:LYS308 4.5 45.6 1.0
O D:MET174 4.6 35.3 1.0
CA D:SER231 4.7 38.4 1.0
CD1 D:LEU173 4.8 61.3 1.0
O C:HOH559 5.0 52.7 1.0
O C:GLN295 5.0 45.4 1.0

Chlorine binding site 4 out of 6 in 5vmt

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Chlorine binding site 4 out of 6 in the Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:47.0
occ:1.00
 NZ D:LYS308 3.2 36.6 1.0
O D:HOH559 3.5 60.8 1.0
CD D:LYS308 3.6 34.9 1.0
CE D:LYS308 3.7 35.8 1.0
CB D:ARG297 3.7 50.6 1.0
C C:GLY230 3.7 50.0 1.0
CG D:ARG297 3.7 50.5 1.0
CA C:GLY230 3.8 46.1 1.0
CB C:SER231 3.8 40.7 1.0
N C:SER231 4.0 45.0 1.0
O C:GLY230 4.1 54.1 1.0
CD D:ARG297 4.4 50.8 1.0
CD2 C:LEU173 4.5 54.2 1.0
N C:GLY230 4.5 47.4 1.0
CA C:SER231 4.6 43.0 1.0
CB D:LYS308 4.6 37.1 1.0
CG D:LYS308 4.7 36.6 1.0
O D:HOH522 4.7 33.7 1.0
O C:MET174 4.7 41.5 1.0
OG C:SER231 4.9 53.3 1.0
O D:GLN295 4.9 40.6 1.0

Chlorine binding site 5 out of 6 in 5vmt

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Chlorine binding site 5 out of 6 in the Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:40.9
occ:1.00
 O E:HOH516 3.0 27.4 1.0
NZ E:LYS308 3.0 27.1 1.0
O E:HOH518 3.3 40.6 1.0
C F:GLY230 3.6 25.8 1.0
CA F:GLY230 3.7 26.1 1.0
CB F:SER231 3.7 30.9 1.0
CE E:LYS308 3.7 32.6 1.0
CB E:ARG297 3.8 28.7 1.0
CD E:LYS308 3.8 37.7 1.0
CG E:ARG297 3.9 38.3 1.0
N F:SER231 3.9 36.0 1.0
O F:GLY230 3.9 29.7 1.0
N F:GLY230 4.3 26.1 1.0
CA F:SER231 4.4 35.0 1.0
CD E:ARG297 4.5 41.7 1.0
CD2 F:LEU173 4.5 28.7 1.0
OG F:SER231 4.6 46.5 1.0
O E:HOH526 4.6 41.4 1.0
O F:MET174 4.7 37.5 1.0
CB E:LYS308 4.7 28.7 1.0
CG E:LYS308 4.8 28.6 1.0

Chlorine binding site 6 out of 6 in 5vmt

Go back to Chlorine Binding Sites List in 5vmt
Chlorine binding site 6 out of 6 in the Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl402

b:54.8
occ:1.00
 NZ F:LYS308 3.1 37.5 1.0
CE F:LYS308 3.5 34.4 1.0
CD F:LYS308 3.6 36.3 1.0
C E:GLY230 3.7 44.1 1.0
CB F:ARG297 3.7 43.9 1.0
CB E:SER231 3.7 45.1 1.0
CA E:GLY230 3.8 43.2 1.0
CG F:ARG297 3.9 50.4 1.0
O E:GLY230 3.9 50.1 1.0
N E:SER231 4.0 44.7 1.0
N E:GLY230 4.5 48.2 1.0
CA E:SER231 4.5 47.1 1.0
O E:MET174 4.5 42.0 1.0
CB F:LYS308 4.5 44.0 1.0
CD F:ARG297 4.5 54.7 1.0
CD2 E:LEU173 4.6 42.1 1.0
CG F:LYS308 4.7 40.5 1.0
OG E:SER231 4.7 52.3 1.0
O F:HOH506 4.9 39.4 1.0
CD1 E:LEU173 4.9 41.2 1.0

Reference:

T.E.Edwards, J.Abendroth, D.D.Lorimer, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of A Glyceraldehyde-3-Phosphate Dehydrogenase From Neisseria Gonorrhoeae Bound to Nad To Be Published.
Page generated: Sat Jul 12 09:57:18 2025

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