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Calcium in PDB 1q9x: Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna

Enzymatic activity of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna

All present enzymatic activity of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna, PDB code: 1q9x was solved by E.Freisinger, A.P.Grollman, H.Miller, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.00 / 2.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 131.948, 122.237, 165.358, 90.00, 96.85, 90.00
R / Rfree (%) 21.5 / 28.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna (pdb code 1q9x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna, PDB code: 1q9x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1q9x

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Calcium binding site 1 out of 8 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:91.7
occ:1.00
 OG A:SER624 2.6 53.6 1.0
OD2 A:ASP623 3.0 56.7 1.0
CG A:ASP623 3.6 54.9 1.0
OD1 A:ASP623 3.6 57.4 1.0
C5' I:DOC953 3.7 84.2 1.0
O5' I:DOC953 3.7 85.8 1.0
CB A:SER624 4.0 51.8 1.0
C3' I:DOC953 4.0 83.7 1.0
C4' I:DOC953 4.1 84.8 1.0
OD2 A:ASP411 4.4 55.2 1.0
N A:SER624 4.4 51.9 1.0
OD1 A:ASP411 4.5 53.1 1.0
CG A:ASP411 4.7 53.2 1.0
O A:ASP621 4.7 53.0 1.0
OP2 I:DOC953 4.8 83.2 1.0
CA A:SER624 4.8 51.6 1.0
P I:DOC953 4.8 85.7 1.0
CB A:ASP623 4.9 53.5 1.0

Calcium binding site 2 out of 8 in 1q9x

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Calcium binding site 2 out of 8 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:67.5
occ:1.00
 O A:HOH1112 2.2 48.5 1.0
OD2 A:ASP684 2.6 66.3 1.0
CG A:ASP684 3.5 63.8 1.0
OD1 A:ASP684 3.5 68.0 1.0
CG A:GLU716 4.4 66.1 1.0
O A:HOH1108 4.4 66.1 1.0
CD A:GLU716 4.5 70.5 1.0
O A:ARG685 4.6 56.5 1.0
OG1 A:THR413 4.7 55.2 1.0
OE2 A:GLU716 4.7 71.0 1.0
O A:ASP684 4.8 56.9 1.0
O A:ASP411 4.8 52.2 1.0
OE2 A:GLU686 4.8 61.0 1.0
OE1 A:GLU716 4.9 70.4 1.0
CB A:ASP684 4.9 61.2 1.0

Calcium binding site 3 out of 8 in 1q9x

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Calcium binding site 3 out of 8 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1003

b:54.8
occ:1.00
 OD2 B:ASP684 2.3 72.2 1.0
CG B:ASP684 3.4 58.8 1.0
OD1 B:ASP684 3.6 65.7 1.0
OE2 B:GLU686 3.8 50.9 1.0
OE1 B:GLU716 4.0 65.8 1.0
OG1 B:THR413 4.3 42.8 1.0
O B:ASP411 4.5 39.8 1.0
CD B:GLU716 4.8 63.5 1.0
CB B:ASP684 4.8 53.1 1.0
CG B:GLU716 4.8 57.2 1.0
O B:ASP684 4.8 46.8 1.0
CB B:ASP411 4.9 40.6 1.0

Calcium binding site 4 out of 8 in 1q9x

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Calcium binding site 4 out of 8 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1004

b:96.7
occ:1.00
 OG B:SER624 2.8 41.5 1.0
OD2 B:ASP623 2.9 42.0 1.0
CG B:ASP623 3.6 41.0 1.0
OD1 B:ASP623 3.7 43.0 1.0
C5' J:DOC953 3.8 46.4 1.0
OD2 B:ASP411 3.8 47.0 1.0
CB B:SER624 4.0 39.4 1.0
CG B:ASP411 4.3 44.3 1.0
C3' J:DOC953 4.4 44.1 1.0
OD1 B:ASP411 4.6 48.6 1.0
C4' J:DOC953 4.6 46.6 1.0
O5' J:DOC953 4.7 43.5 1.0
OP2 J:DOC953 4.9 45.0 1.0

Calcium binding site 5 out of 8 in 1q9x

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Calcium binding site 5 out of 8 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1005

b:75.7
occ:1.00
 OD1 C:ASP623 2.8 31.6 1.0
O C:HOH1093 3.1 48.1 1.0
OP1 G:DGP908 3.2 83.2 1.0
CG C:ASP623 3.4 33.3 1.0
OD2 C:ASP623 3.5 35.2 1.0
OD1 C:ASP411 3.6 38.1 1.0
CG C:ASP411 4.2 36.7 1.0
P G:DGP908 4.4 85.5 1.0
OG C:SER624 4.5 36.9 1.0
O C:LEU412 4.6 31.1 1.0
CB C:ASP411 4.6 33.5 1.0
CB C:ASP623 4.6 32.8 1.0
OD2 C:ASP411 4.8 41.3 1.0
O5' G:DGP908 4.9 82.5 1.0
O C:ASP623 4.9 34.0 1.0

Calcium binding site 6 out of 8 in 1q9x

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Calcium binding site 6 out of 8 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1006

b:57.2
occ:1.00
 OD2 C:ASP684 2.3 63.1 1.0
CG C:ASP684 3.1 48.2 1.0
OD1 C:ASP684 3.2 54.4 1.0
OE1 C:GLU716 3.6 56.8 1.0
OE2 C:GLU686 4.3 50.5 1.0
CG C:GLU716 4.3 47.2 1.0
CD C:GLU716 4.4 54.9 1.0
O C:ASP411 4.4 32.8 1.0
OG1 C:THR413 4.5 37.5 1.0
CB C:ASP411 4.5 33.5 1.0
CB C:ASP684 4.6 42.4 1.0
O C:ASP684 4.7 38.0 1.0
N C:ASP684 5.0 38.9 1.0
C C:ASP684 5.0 38.8 1.0
O C:ARG685 5.0 36.6 1.0

Calcium binding site 7 out of 8 in 1q9x

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Calcium binding site 7 out of 8 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1007

b:56.0
occ:1.00
 OD2 D:ASP684 2.3 67.1 1.0
O D:HOH1091 2.8 65.9 1.0
OG1 D:THR413 2.9 41.7 1.0
CG D:ASP684 3.1 52.7 1.0
OD1 D:ASP684 3.3 57.5 1.0
O D:ASP411 3.3 37.4 1.0
N D:ASP684 4.2 43.7 1.0
CB D:THR413 4.2 37.6 1.0
C D:ASP411 4.2 36.9 1.0
N D:THR413 4.3 35.8 1.0
CB D:ASP684 4.4 48.0 1.0
CB D:ASP411 4.4 38.4 1.0
CA D:THR413 4.4 36.2 1.0
O D:ASP684 4.5 42.9 1.0
CA D:ASP684 4.6 45.7 1.0
O D:PHE682 4.6 39.4 1.0
C D:LEU412 4.7 34.9 1.0
CA D:ASP411 4.8 37.8 1.0
C D:ASP684 4.8 44.3 1.0

Calcium binding site 8 out of 8 in 1q9x

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Calcium binding site 8 out of 8 in the Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Enterobacteria Phage RB69 GP43 Dna Polymerase Complexed with Tetrahydrofuran Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1008

b:79.0
occ:1.00
 OG D:SER624 3.0 41.9 1.0
OD2 D:ASP623 3.3 44.9 1.0
OD1 D:ASP623 3.5 38.1 1.0
OD2 D:ASP411 3.6 46.3 1.0
CG D:ASP623 3.7 39.5 1.0
C5' L:DOC953 4.0 48.6 1.0
CG D:ASP411 4.1 42.7 1.0
OD1 D:ASP411 4.1 45.5 1.0
CB D:SER624 4.3 38.9 1.0
OP2 L:DOC953 4.5 49.2 1.0
C3' L:DOC953 4.6 43.6 1.0
O5' L:DOC953 4.8 48.6 1.0
C4' L:DOC953 4.8 47.0 1.0

Reference:

E.Freisinger, A.P.Grollman, H.Miller, C.Kisker. Lesion (in)Tolerance Reveals Insights Into Dna Replication Fidelity. Embo J. V. 23 1494 2004.
ISSN: ISSN 0261-4189
PubMed: 15057282
DOI: 10.1038/SJ.EMBOJ.7600158
Page generated: Thu Jul 11 14:11:45 2024

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