Atomistry » Manganese » PDB 3rla-3sx3 » 3sq0
Atomistry »
  Manganese »
    PDB 3rla-3sx3 »
      3sq0 »

Manganese in PDB 3sq0: Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)

Enzymatic activity of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)

All present enzymatic activity of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+), PDB code: 3sq0 was solved by S.Xia, W.H.Konigsberg, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.24 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.146, 119.669, 130.639, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) (pdb code 3sq0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+), PDB code: 3sq0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 1 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn905

b:30.4
occ:1.00
 OD1 A:ASP623 2.0 29.1 1.0
OD1 A:ASP411 2.1 30.0 1.0
O2B A:DUP904 2.1 27.8 1.0
O1G A:DUP904 2.1 31.4 1.0
O A:LEU412 2.2 31.8 1.0
O2A A:DUP904 2.3 30.6 1.0
CG A:ASP623 3.1 29.4 1.0
CG A:ASP411 3.2 31.9 1.0
PB A:DUP904 3.2 27.2 1.0
C A:LEU412 3.3 30.5 1.0
PG A:DUP904 3.4 30.6 1.0
MN A:MN906 3.4 32.4 1.0
PA A:DUP904 3.5 30.9 1.0
OD2 A:ASP623 3.6 28.6 1.0
N3A A:DUP904 3.6 30.6 1.0
O3B A:DUP904 3.7 30.8 1.0
OD2 A:ASP411 3.7 31.2 1.0
N A:LEU412 3.9 31.6 1.0
O A:HOH978 3.9 28.9 1.0
CA A:LEU412 4.1 29.7 1.0
C5' A:DUP904 4.1 27.4 1.0
O2G A:DUP904 4.1 30.2 1.0
N A:SER414 4.3 27.1 1.0
O5' A:DUP904 4.3 31.6 1.0
N A:THR413 4.4 29.7 1.0
CB A:ASP623 4.4 29.4 1.0
CB A:ASP411 4.4 28.8 1.0
N A:LEU415 4.5 27.9 1.0
C A:ASP411 4.5 30.7 1.0
CB A:LEU412 4.6 30.4 1.0
O A:HOH922 4.6 27.0 1.0
O1B A:DUP904 4.6 30.4 1.0
C A:THR413 4.6 29.0 1.0
CA A:THR413 4.6 31.1 1.0
O1A A:DUP904 4.7 30.9 1.0
CB A:LEU415 4.8 27.5 1.0
O3G A:DUP904 4.9 33.4 1.0
O A:ASP623 4.9 30.9 1.0
CA A:SER414 4.9 30.2 1.0
CA A:ASP411 5.0 30.3 1.0

Manganese binding site 2 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 2 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn906

b:32.4
occ:1.00
 OD2 A:ASP623 2.1 28.6 1.0
O2A A:DUP904 2.1 30.6 1.0
O A:HOH922 2.1 27.0 1.0
OD2 A:ASP411 2.1 31.2 1.0
O A:HOH1118 2.3 25.3 1.0
CG A:ASP411 3.0 31.9 1.0
CG A:ASP623 3.0 29.4 1.0
OD1 A:ASP411 3.1 30.0 1.0
OD1 A:ASP623 3.2 29.1 1.0
PA A:DUP904 3.3 30.9 1.0
MN A:MN905 3.4 30.4 1.0
O1A A:DUP904 3.7 30.9 1.0
C3' P:DOC115 3.9 35.2 1.0
O5' A:DUP904 3.9 31.6 1.0
O A:HOH1115 4.1 37.4 1.0
C5' A:DUP904 4.1 27.4 1.0
CB A:SER624 4.3 30.5 1.0
C A:ASP623 4.4 30.8 1.0
CB A:ASP623 4.4 29.4 1.0
O P:HOH226 4.4 27.9 1.0
O A:ASP621 4.4 32.3 1.0
CB A:ASP411 4.4 28.8 1.0
O1G A:DUP904 4.5 31.4 1.0
N A:SER624 4.5 28.2 1.0
O A:ASP623 4.5 30.9 1.0
N3A A:DUP904 4.7 30.6 1.0
N A:ASP623 4.7 28.8 1.0
OG A:SER624 4.7 29.9 1.0
CA A:ASP623 4.7 30.8 1.0
O2B A:DUP904 4.8 27.8 1.0
CA A:SER624 4.9 31.6 1.0
C5' P:DOC115 4.9 40.9 1.0
C4' P:DOC115 4.9 37.2 1.0
C2' P:DOC115 5.0 34.9 1.0

Manganese binding site 3 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 3 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn907

b:53.9
occ:1.00
 O A:HOH978 2.3 28.9 1.0
O A:HOH1070 2.3 45.8 1.0
OE1 A:GLU686 2.5 50.7 1.0
O A:HOH1073 2.7 36.2 1.0
OE1 A:GLU716 3.1 57.0 1.0
CD A:GLU686 3.5 49.9 1.0
O A:HOH1123 3.7 32.4 1.0
OE2 A:GLU686 3.8 55.6 1.0
CD A:GLU716 3.8 53.1 1.0
OD2 A:ASP684 4.1 51.2 1.0
OE2 A:GLU716 4.2 55.2 1.0
O A:HOH1089 4.2 39.6 1.0
CB A:ASP684 4.2 41.8 1.0
O A:ASP411 4.3 32.1 1.0
NZ A:LYS486 4.3 46.3 1.0
O2G A:DUP904 4.4 30.2 1.0
OG1 A:THR413 4.4 36.7 1.0
CG A:ASP684 4.5 50.0 1.0
O1G A:DUP904 4.6 31.4 1.0
CB A:ASP411 4.7 28.8 1.0
CG A:GLU686 4.7 43.2 1.0
OD1 A:ASP411 4.7 30.0 1.0
CE A:LYS486 4.8 38.6 1.0
CG A:GLU716 4.8 49.6 1.0
PG A:DUP904 4.8 30.6 1.0
CA A:THR413 4.9 31.1 1.0
C A:ASP411 5.0 30.7 1.0

Manganese binding site 4 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 4 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn908

b:52.3
occ:1.00
 O A:HOH934 2.0 39.1 1.0
OE2 A:GLU116 2.1 43.9 1.0
O A:HOH1139 2.2 48.0 1.0
OD2 A:ASP114 2.4 48.1 1.0
CD A:GLU116 3.1 40.3 1.0
OE1 A:GLU116 3.3 43.4 1.0
CG A:ASP114 3.3 41.9 1.0
OD1 A:ASP114 3.5 46.2 1.0
ND2 A:ASN324 4.2 38.5 1.0
O A:ILE115 4.3 36.2 1.0
CB A:ALA327 4.3 32.0 1.0
CG A:GLU116 4.4 37.0 1.0
CA A:ASN324 4.7 36.0 1.0
CB A:ASP114 4.7 37.1 1.0
C A:ILE115 5.0 36.4 1.0

Manganese binding site 5 out of 5 in 3sq0

Go back to Manganese Binding Sites List in 3sq0
Manganese binding site 5 out of 5 in the Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dna Polymerase(L561A/S565G/Y567A) Ternary Complex with Dupnpp Opposite Da (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn909

b:0.8
occ:1.00
 OE2 A:GLU160 3.9 70.1 1.0
CD1 A:LEU152 4.5 47.2 1.0
OD1 A:ASP192 4.6 66.5 1.0
OE2 A:GLU161 4.8 68.7 1.0
CD A:GLU160 4.9 69.5 1.0

Reference:

S.Xia, M.Wang, G.Blaha, W.H.Konigsberg, J.Wang. Structural Insights Into Complete Metal Ion Coordination From Ternary Complexes of B Family RB69 Dna Polymerase. Biochemistry V. 50 9114 2011.
ISSN: ISSN 0006-2960
PubMed: 21923197
DOI: 10.1021/BI201260H
Page generated: Sat Oct 5 17:54:33 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