Atomistry » Manganese » PDB 7fqa-7kst » 7k97
Atomistry »
  Manganese »
    PDB 7fqa-7kst »
      7k97 »

Manganese in PDB 7k97: Human Dna Polymerase Beta Dgdp Product Complex with MN2+

Enzymatic activity of Human Dna Polymerase Beta Dgdp Product Complex with MN2+

All present enzymatic activity of Human Dna Polymerase Beta Dgdp Product Complex with MN2+:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Dgdp Product Complex with MN2+, PDB code: 7k97 was solved by F.A.Varela, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.58 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.102, 77.309, 55.111, 90, 114.85, 90
R / Rfree (%) 18.5 / 24

Other elements in 7k97:

The structure of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+ (pdb code 7k97). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+, PDB code: 7k97:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 1 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:25.6
occ:0.89
 OD2 A:ASP190 1.9 24.1 1.0
OD1 A:ASP192 2.1 29.1 1.0
OD2 A:ASP256 2.3 24.8 1.0
OP1 P:DG11 2.4 27.6 1.0
O3' P:DC10 2.4 41.9 1.0
CG A:ASP190 2.8 26.7 1.0
P P:DG11 2.9 35.5 1.0
CG A:ASP192 3.0 26.9 1.0
OD1 A:ASP190 3.1 35.6 1.0
MN A:MN402 3.3 34.2 0.9
OD2 A:ASP192 3.3 29.2 1.0
CG A:ASP256 3.4 24.4 1.0
C3' P:DC10 3.7 33.6 1.0
C4' P:DC10 3.9 33.5 1.0
OP2 P:DG11 4.0 42.0 1.0
CB A:ASP256 4.0 26.1 1.0
C5' P:DC10 4.1 30.9 1.0
O5' P:DG11 4.1 33.3 1.0
CB A:ASP190 4.2 26.1 1.0
C5' P:DG11 4.2 29.9 1.0
CB A:ASP192 4.4 24.7 1.0
OD1 A:ASP256 4.4 26.2 1.0
O1 P:PO4103 4.7 39.7 1.0
C2' P:DC10 4.7 29.1 1.0
OP1 P:DC10 4.7 28.3 1.0
O A:MET191 4.9 25.3 1.0
CA A:ASP192 4.9 28.1 1.0
O5' P:DC10 4.9 30.4 1.0
NH2 A:ARG254 5.0 31.4 1.0

Manganese binding site 2 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 2 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:34.2
occ:0.91
 O1 P:PO4103 1.8 39.7 1.0
OP1 P:DG11 1.9 27.6 1.0
OD1 A:ASP190 2.0 35.6 1.0
OD2 A:ASP192 2.0 29.2 1.0
O P:HOH203 2.4 33.0 1.0
CG A:ASP190 3.0 26.7 1.0
CG A:ASP192 3.0 26.9 1.0
P P:PO4103 3.1 44.2 1.0
MN A:MN401 3.3 25.6 0.9
P P:DG11 3.3 35.5 1.0
OD1 A:ASP192 3.4 29.1 1.0
OD2 A:ASP190 3.4 24.1 1.0
O4 P:PO4103 3.5 47.8 1.0
O5' P:DG11 3.8 33.3 1.0
O2 P:PO4103 3.9 37.9 1.0
C5' P:DG11 4.0 29.9 1.0
O3 P:PO4103 4.1 37.5 1.0
N A:ASP190 4.2 24.9 1.0
OP2 P:DG11 4.2 42.0 1.0
O3' P:DC10 4.3 41.9 1.0
CB A:ASP190 4.3 26.1 1.0
CB A:ASP192 4.4 24.7 1.0
CA A:ASP190 4.6 29.5 1.0
C A:ASP190 4.6 32.9 1.0
CA A:GLY179 4.6 27.1 1.0
N A:SER180 4.7 34.2 1.0
O A:ASP190 4.8 32.8 1.0
N A:ASP192 5.0 27.9 1.0
N A:MET191 5.0 28.5 1.0

Manganese binding site 3 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 3 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:76.1
occ:1.00
 OD1 A:ASP124 2.2 64.0 1.0
CG A:ASP124 3.0 55.3 1.0
OD2 A:ASP124 3.2 55.8 1.0
OG1 A:THR121 3.9 50.9 1.0
CB A:ASP124 4.4 44.6 1.0
N A:ASP124 4.7 46.1 1.0
CA A:ASP124 4.8 45.5 1.0
OE1 A:GLU123 5.0 69.0 1.0

Manganese binding site 4 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 4 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:86.7
occ:1.00
 CE1 A:HIS285 2.0 69.9 1.0
ND1 A:HIS285 2.0 64.1 1.0
OE1 A:GLU288 3.0 68.6 1.0
O A:HOH533 3.1 62.4 1.0
NE2 A:HIS285 3.3 82.7 1.0
CG A:HIS285 3.4 60.0 1.0
OE2 A:GLU288 3.5 75.4 1.0
CD A:GLU288 3.6 71.4 1.0
CD2 A:HIS285 4.0 59.5 1.0
CB A:HIS285 4.4 43.3 1.0
CA A:HIS285 4.7 46.8 1.0

Manganese binding site 5 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 5 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:93.6
occ:1.00
 NE2 A:HIS222 2.3 69.4 1.0
CE1 A:HIS222 3.1 64.1 1.0
CD2 A:HIS222 3.5 50.3 1.0
ND1 A:HIS222 4.3 64.7 1.0
CG A:HIS222 4.5 50.9 1.0

Manganese binding site 6 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 6 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:74.1
occ:1.00
 N7 P:DG4 2.2 61.4 1.0
C8 P:DG4 3.2 60.8 1.0
C5 P:DG4 3.3 55.4 1.0
O6 P:DG4 3.5 49.8 1.0
C6 P:DG4 3.8 50.6 1.0
O4 T:DT12 4.3 38.3 1.0
C2' P:DT3 4.3 55.4 1.0
N6 P:DA5 4.4 46.4 1.0
N9 P:DG4 4.4 53.8 1.0
C4 P:DG4 4.4 53.1 1.0

Manganese binding site 7 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 7 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn102

b:82.5
occ:1.00
 OP2 P:DG11 2.2 42.0 1.0
O4 P:PO4103 3.0 47.8 1.0
P P:DG11 3.6 35.5 1.0
O5' P:DG11 4.1 33.3 1.0
OD2 A:ASP276 4.2 42.8 1.0
OP1 P:DG11 4.4 27.6 1.0
P P:PO4103 4.5 44.2 1.0
O3' P:DC10 4.8 41.9 1.0
OP2 P:DC10 4.8 29.2 1.0
C8 P:DG11 4.8 29.3 1.0
N7 P:DG11 4.9 32.4 1.0

Manganese binding site 8 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 8 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:66.2
occ:1.00
 O T:HOH205 2.7 51.1 1.0
N7 T:DG3 3.1 68.2 1.0
O6 T:DG3 3.3 58.7 1.0
C5 T:DG3 3.8 61.8 1.0
C6 T:DG3 3.9 57.9 1.0
C8 T:DG3 4.2 67.5 1.0
O4 D:DT2 4.2 42.7 1.0
N6 T:DA4 4.9 44.5 1.0
C6 T:DC2 5.0 59.3 1.0

Reference:

F.A.Varela, B.D.Freudenthal. Mechanism of Deoxyguanosine Diphosphate Insertion By Human Dna Polymerase Beta. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33475337
DOI: 10.1021/ACS.BIOCHEM.0C00847
Page generated: Sun Oct 6 08:55:19 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