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Chlorine in PDB 2fms: Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site

Enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site, PDB code: 2fms was solved by V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.91 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 19.6 / 24.4

Other elements in 2fms:

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site (pdb code 2fms). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site, PDB code: 2fms:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2fms

Go back to Chlorine Binding Sites List in 2fms
Chlorine binding site 1 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:38.5
occ:1.00
 O A:HOH392 3.1 33.2 1.0
N A:CYS267 3.3 26.0 1.0
CA A:GLN264 3.5 27.9 1.0
C A:GLN264 3.5 29.1 1.0
N A:TYR266 3.6 31.4 1.0
CB A:TYR266 3.7 33.7 1.0
SG A:CYS267 3.8 29.0 1.0
CG1 A:VAL313 3.8 33.9 1.0
O A:GLN264 3.8 28.2 1.0
CB A:VAL313 3.9 33.0 1.0
CA A:TYR266 3.9 30.4 1.0
O A:ASP263 4.0 31.8 1.0
N A:TYR265 4.0 29.2 1.0
CB A:CYS267 4.0 29.1 1.0
C A:TYR266 4.1 27.9 1.0
CA A:CYS267 4.3 25.9 1.0
CD2 A:TYR266 4.4 38.8 1.0
O A:TYR296 4.4 23.7 1.0
CB A:GLN264 4.4 29.3 1.0
N A:GLN264 4.4 29.3 1.0
C A:TYR265 4.5 30.6 1.0
O A:VAL313 4.5 35.7 1.0
CG A:TYR266 4.5 37.6 1.0
C A:ASP263 4.6 30.9 1.0
CG2 A:VAL313 4.8 32.4 1.0
CA A:TYR265 4.8 30.5 1.0
CG A:GLN264 5.0 28.7 1.0
C A:VAL313 5.0 36.2 1.0

Chlorine binding site 2 out of 4 in 2fms

Go back to Chlorine Binding Sites List in 2fms
Chlorine binding site 2 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:43.2
occ:1.00
 N A:HIS34 3.1 32.6 1.0
CB A:HIS34 3.3 32.0 1.0
C A:ALA32 3.4 32.8 1.0
N A:LYS35 3.5 28.8 1.0
CA A:ALA32 3.5 32.3 1.0
CB A:ALA32 3.5 28.9 1.0
CA A:HIS34 3.6 32.2 1.0
O A:HOH584 3.7 45.1 1.0
N A:ILE33 3.7 32.1 1.0
O A:ALA32 3.8 32.7 1.0
CD2 A:HIS34 3.8 33.9 1.0
CG A:HIS34 3.9 35.2 1.0
C A:HIS34 4.0 31.1 1.0
CG A:LYS35 4.1 30.7 1.0
C A:ILE33 4.2 32.8 1.0
O A:HOH441 4.4 35.4 1.0
CA A:ILE33 4.5 33.7 1.0
CB A:LYS35 4.5 28.2 1.0
CA A:LYS35 4.6 28.1 1.0
O6 D:DG1 4.8 37.9 1.0
CG2 A:ILE33 4.9 36.6 1.0
CD A:LYS35 5.0 34.2 1.0
N A:ALA32 5.0 31.5 1.0

Chlorine binding site 3 out of 4 in 2fms

Go back to Chlorine Binding Sites List in 2fms
Chlorine binding site 3 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:48.2
occ:1.00
 N A:LEU82 3.2 35.3 1.0
NH1 A:ARG89 3.4 54.3 1.0
NH2 A:ARG89 3.6 54.8 1.0
CA A:LYS81 3.8 38.3 1.0
CB A:LYS81 3.9 42.4 1.0
CZ A:ARG89 3.9 52.1 1.0
O A:LEU82 3.9 35.8 1.0
C A:LYS81 3.9 36.5 1.0
CB A:LEU85 4.0 34.8 1.0
CB A:LEU82 4.0 37.2 1.0
CA A:LEU82 4.1 36.1 1.0
CD1 A:LEU85 4.2 31.2 1.0
C A:LEU82 4.4 36.5 1.0
CG A:LEU85 4.7 33.5 1.0
N A:GLU86 4.9 37.3 1.0
CG A:GLU86 5.0 49.2 1.0

Chlorine binding site 4 out of 4 in 2fms

Go back to Chlorine Binding Sites List in 2fms
Chlorine binding site 4 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Magnesium in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl346

b:36.3
occ:1.00
 NH2 A:ARG299 2.9 28.1 0.5
O A:HOH500 3.0 43.0 1.0
ND2 A:ASN294 3.2 28.0 1.0
NE A:ARG299 3.4 30.9 0.5
OG1 A:THR297 3.4 32.3 1.0
CZ A:ARG299 3.6 31.3 0.5
NH1 A:ARG299 3.6 40.7 0.5
CZ A:ARG299 3.8 40.6 0.5
CB A:TYR296 4.1 29.1 1.0
CG A:ASN294 4.1 30.0 1.0
NH2 A:ARG299 4.2 40.4 0.5
OD1 A:ASN294 4.2 28.8 1.0
CD2 A:TYR296 4.2 29.2 1.0
CG2 A:THR297 4.2 32.9 1.0
NE A:ARG299 4.3 39.2 0.5
CB A:THR297 4.4 33.3 1.0
CG A:TYR296 4.6 27.9 1.0
CD A:ARG299 4.7 31.8 0.5
CD A:ARG299 4.7 37.5 0.5
O A:HOH413 4.8 35.2 1.0
N A:THR297 4.8 27.2 1.0
O A:HOH524 4.9 56.0 1.0
NH1 A:ARG299 4.9 31.9 0.5
O T:HOH42 4.9 39.6 1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson. Magnesium-Induced Assembly of A Complete Dna Polymerase Catalytic Complex. Structure V. 14 757 2006.
ISSN: ISSN 0969-2126
PubMed: 16615916
DOI: 10.1016/J.STR.2006.01.011
Page generated: Sat Dec 12 09:05:10 2020

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