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Manganese in PDB 3sjj: RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+

Enzymatic activity of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+

All present enzymatic activity of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+, PDB code: 3sjj was solved by M.Wang, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.25 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.560, 118.217, 130.108, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 26.5

Manganese Binding Sites:

The binding sites of Manganese atom in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+ (pdb code 3sjj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+, PDB code: 3sjj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 3sjj

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Manganese binding site 1 out of 7 in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn905

b:40.1
occ:1.00
 O2B A:DUP904 2.1 15.1 1.0
OD1 A:ASP623 2.1 32.2 1.0
OD1 A:ASP411 2.1 42.7 1.0
O2A A:DUP904 2.1 21.9 1.0
O1G A:DUP904 2.3 13.3 1.0
O A:LEU412 2.3 43.5 1.0
CG A:ASP411 3.0 39.9 1.0
MN A:MN906 3.2 39.3 1.0
OD2 A:ASP411 3.2 40.6 1.0
PB A:DUP904 3.2 17.0 1.0
CG A:ASP623 3.3 34.9 1.0
C A:LEU412 3.4 38.6 1.0
PA A:DUP904 3.5 24.1 1.0
O A:HOH969 3.5 36.4 1.0
PG A:DUP904 3.5 16.3 1.0
O3B A:DUP904 3.7 18.6 1.0
N3A A:DUP904 3.7 10.7 1.0
O A:HOH978 3.8 42.7 1.0
N A:LEU412 3.9 40.7 1.0
OD2 A:ASP623 3.9 40.9 1.0
C5' A:DUP904 4.0 22.1 1.0
CA A:LEU412 4.1 36.8 1.0
O5' A:DUP904 4.2 22.6 1.0
O2G A:DUP904 4.4 13.7 1.0
CB A:ASP411 4.4 38.4 1.0
N A:SER414 4.5 31.9 1.0
C A:ASP411 4.5 41.1 1.0
CB A:ASP623 4.5 33.2 1.0
N A:THR413 4.5 36.1 1.0
CB A:LEU412 4.5 36.1 1.0
N A:LEU415 4.6 30.8 1.0
O3G A:DUP904 4.6 23.2 1.0
O1B A:DUP904 4.6 15.8 1.0
O1A A:DUP904 4.7 16.3 1.0
C A:THR413 4.7 32.0 1.0
O A:HOH968 4.7 19.2 1.0
CA A:THR413 4.7 35.7 1.0
CB A:LEU415 4.8 34.1 1.0
CA A:ASP411 4.9 38.7 1.0
O P:HOH138 4.9 8.2 1.0
O A:ASP623 4.9 29.9 1.0

Manganese binding site 2 out of 7 in 3sjj

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Manganese binding site 2 out of 7 in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn906

b:39.3
occ:1.00
 O P:HOH138 1.8 8.2 1.0
O2A A:DUP904 2.0 21.9 1.0
OD2 A:ASP623 2.1 40.9 1.0
OD2 A:ASP411 2.2 40.6 1.0
O A:HOH968 2.4 19.2 1.0
O3' P:DC115 2.5 43.0 1.0
OD1 A:ASP623 2.8 32.2 1.0
CG A:ASP623 2.8 34.9 1.0
PA A:DUP904 3.0 24.1 1.0
MN A:MN905 3.2 40.1 1.0
CG A:ASP411 3.2 39.9 1.0
O5' A:DUP904 3.3 22.6 1.0
O A:HOH969 3.4 36.4 1.0
O1A A:DUP904 3.5 16.3 1.0
C3' P:DC115 3.5 45.5 1.0
OD1 A:ASP411 3.6 42.7 1.0
C5' A:DUP904 3.7 22.1 1.0
CB A:ASP623 4.3 33.2 1.0
N3A A:DUP904 4.4 10.7 1.0
O2B A:DUP904 4.5 15.1 1.0
CB A:ASP411 4.5 38.4 1.0
O1G A:DUP904 4.6 13.3 1.0
O A:ASP621 4.6 44.8 1.0
C2' P:DC115 4.6 44.4 1.0
C4' P:DC115 4.6 43.1 1.0
C A:ASP623 4.6 30.4 1.0
O A:ASP623 4.7 29.9 1.0
CB A:SER624 4.7 35.2 1.0
C5' P:DC115 4.8 43.8 1.0
O A:HOH993 4.8 22.1 1.0
CA A:ASP623 4.9 34.2 1.0
N A:SER624 4.9 31.5 1.0
N A:ASP623 4.9 36.4 1.0

Manganese binding site 3 out of 7 in 3sjj

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Manganese binding site 3 out of 7 in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn907

b:86.9
occ:1.00
 O A:HOH976 2.0 87.5 1.0
O A:HOH978 2.2 42.7 1.0
OE1 A:GLU716 3.0 72.7 1.0
CD A:GLU716 3.5 70.5 1.0
MN A:MN910 3.5 81.5 1.0
OE2 A:GLU716 3.7 71.8 1.0
O A:HOH1005 4.1 22.2 1.0
NZ A:LYS486 4.1 44.1 1.0
O A:ASP411 4.1 42.8 1.0
CB A:ASP684 4.2 59.4 1.0
OG1 A:THR413 4.4 43.9 1.0
OD1 A:ASP411 4.4 42.7 1.0
O1G A:DUP904 4.4 13.3 1.0
CG A:GLU716 4.6 59.9 1.0
O2G A:DUP904 4.7 13.7 1.0
CE A:LYS486 4.8 40.7 1.0
CB A:ASP411 4.8 38.4 1.0
CG A:GLU686 4.9 51.7 1.0
C A:ASP411 4.9 41.1 1.0
OD1 A:ASP684 4.9 72.3 1.0
CG A:ASP684 4.9 67.5 1.0
PG A:DUP904 4.9 16.3 1.0
CA A:THR413 4.9 35.7 1.0
OE1 A:GLU686 5.0 58.6 1.0

Manganese binding site 4 out of 7 in 3sjj

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Manganese binding site 4 out of 7 in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn908

b:76.6
occ:1.00
 OE2 A:GLU116 2.1 51.4 1.0
OD2 A:ASP114 2.2 56.2 1.0
CD A:GLU116 3.1 45.8 1.0
CG A:ASP114 3.2 50.2 1.0
OE1 A:GLU116 3.5 45.5 1.0
OD1 A:ASP114 3.5 55.0 1.0
ND2 A:ASN324 4.0 44.0 1.0
O A:ILE115 4.1 41.6 1.0
CB A:ALA327 4.4 36.7 1.0
CG A:GLU116 4.5 41.5 1.0
CB A:ASP114 4.6 39.3 1.0
CA A:ASN324 4.9 38.8 1.0

Manganese binding site 5 out of 7 in 3sjj

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Manganese binding site 5 out of 7 in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn909

b:87.3
occ:1.00
 OE2 A:GLU160 2.2 71.6 1.0
O A:HOH916 2.2 20.4 1.0
O A:HOH964 2.6 12.3 1.0
O A:HOH914 3.0 18.5 1.0
O A:HOH912 3.3 9.6 1.0
CD A:GLU160 3.3 71.3 1.0
O A:HOH970 3.4 27.2 1.0
OE1 A:GLU160 3.8 71.7 1.0
OE2 A:GLU161 4.0 78.6 1.0
O A:HOH913 4.0 16.9 1.0
O A:HOH915 4.2 22.2 1.0
CG A:GLU160 4.6 68.4 1.0
CD A:GLU161 4.8 74.5 1.0
CG A:GLU161 4.8 67.5 1.0

Manganese binding site 6 out of 7 in 3sjj

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Manganese binding site 6 out of 7 in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn910

b:81.5
occ:1.00
 OE1 A:GLU686 2.4 58.6 1.0
O A:HOH978 2.5 42.7 1.0
O A:HOH1005 2.5 22.2 1.0
O A:HOH969 2.9 36.4 1.0
CD A:GLU686 3.5 59.5 1.0
MN A:MN907 3.5 86.9 1.0
OE2 A:GLU716 3.6 71.8 1.0
O1G A:DUP904 3.9 13.3 1.0
CG A:GLU686 3.9 51.7 1.0
O3G A:DUP904 4.0 23.2 1.0
OD1 A:ASP411 4.0 42.7 1.0
CG A:ASP411 4.3 39.9 1.0
CB A:ASP411 4.4 38.4 1.0
CD A:GLU716 4.4 70.5 1.0
PG A:DUP904 4.5 16.3 1.0
OE1 A:GLU716 4.5 72.7 1.0
OE2 A:GLU686 4.5 60.2 1.0
O A:HOH976 4.8 87.5 1.0
CE A:MET715 4.8 56.3 1.0
OD2 A:ASP411 4.9 40.6 1.0

Manganese binding site 7 out of 7 in 3sjj

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Manganese binding site 7 out of 7 in the RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of RB69 Dna Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn911

b:90.0
occ:1.00
 OE1 A:GLU172 2.5 66.0 1.0
CD A:GLU172 3.5 62.6 1.0
OE2 A:GLU172 3.9 63.7 1.0
OE2 A:GLU177 4.3 65.3 1.0
OE1 A:GLU177 4.5 64.3 1.0
CG A:GLU172 4.8 57.8 1.0
CD A:GLU177 4.9 60.0 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 17:53:23 2024

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