Atomistry » Chlorine » PDB 2f81-2fq1 » 2fms
Atomistry »
  Chlorine »
    PDB 2f81-2fq1 »
      2fms »

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 Jul 20 07:09:25 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy