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Calcium in PDB 1clq: Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution

Enzymatic activity of Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution

All present enzymatic activity of Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution, PDB code: 1clq was solved by Y.Shamoo, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.70
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 209.740, 209.740, 114.250, 90.00, 90.00, 120.00
R / Rfree (%) 23 / 28.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution (pdb code 1clq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution, PDB code: 1clq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1clq

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Calcium binding site 1 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


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 A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1024

b:0.1
occ:1.00
 O3' E:DA10 2.3 0.1 1.0
C5' E:DC11 2.5 0.6 1.0
C2' E:DC11 2.6 0.7 1.0
C3' E:DC11 2.9 0.9 1.0
O5' E:DC11 3.0 0.1 1.0
P E:DC11 3.1 0.1 1.0
C4' E:DC11 3.1 0.3 1.0
C6 E:DC11 3.2 0.2 1.0
C2' E:DA10 3.3 0.3 1.0
C1' E:DA10 3.4 0.1 1.0
C3' E:DA10 3.4 0.8 1.0
OP2 E:DC11 3.4 0.1 1.0
C1' E:DC11 3.5 0.8 1.0
O4' E:DC11 3.6 0.6 1.0
N1 E:DC11 3.8 0.6 1.0
O4' E:DA10 4.1 0.1 1.0
C5 E:DC11 4.2 0.9 1.0
O3' E:DC11 4.2 0.9 1.0
C4' E:DA10 4.3 0.0 1.0
N9 E:DA10 4.4 0.7 1.0
OP1 E:DC11 4.4 0.1 1.0
N3 E:DA10 4.8 0.2 1.0
C4 E:DA10 4.9 0.7 1.0

Calcium binding site 2 out of 9 in 1clq

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Calcium binding site 2 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


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 A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1003

b:73.4
occ:1.00
 OD1 A:ASP114 2.1 86.8 1.0
OP1 D:DG1 2.7 59.0 1.0
CG A:ASP114 2.7 76.5 1.0
O A:HOH1185 2.7 53.4 1.0
OD2 A:ASP114 2.8 77.8 1.0
O3' D:DC2 2.9 38.3 1.0
P D:DG1 3.4 49.1 1.0
O A:ILE115 4.0 62.9 1.0
CB A:ASP114 4.1 64.2 1.0
CA A:CA1002 4.1 98.0 1.0
C3' D:DC2 4.2 37.8 1.0
C4' D:DC2 4.4 38.0 1.0
O5' D:DG1 4.4 54.2 1.0
C5' D:DG1 4.4 55.2 1.0
OD1 A:ASP222 4.5 49.7 1.0
OP2 D:DG1 4.5 60.1 1.0
OD2 A:ASP222 4.5 53.0 1.0
N A:ILE115 4.7 56.2 1.0
C2' D:DC2 4.7 43.7 1.0
CA A:ASP114 4.8 56.6 1.0
O A:TRP216 4.9 44.7 1.0
CG A:ASP222 4.9 49.0 1.0
OE2 A:GLU116 5.0 70.7 1.0
CE2 A:PHE221 5.0 43.6 1.0

Calcium binding site 3 out of 9 in 1clq

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Calcium binding site 3 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


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 A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1009

b:78.4
occ:1.00
 O5' D:DT7 2.9 0.4 1.0
OP2 D:DT7 3.0 0.1 1.0
P D:DT7 3.6 0.9 1.0
C5' D:DT7 3.7 0.4 1.0
C4' D:DT7 3.9 0.7 1.0
O3' D:DT7 4.2 0.2 1.0
C3' D:DT7 4.4 0.1 1.0
SD A:MET256 4.6 0.1 1.0
O3' D:DG8 4.7 0.8 1.0
OP1 D:DT7 4.7 0.9 1.0

Calcium binding site 4 out of 9 in 1clq

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Calcium binding site 4 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


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 A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:63.8
occ:1.00
 O A:LYS531 2.2 63.2 1.0
O A:ASN505 2.3 45.9 1.0
OD1 A:ASN507 2.4 69.9 1.0
C A:LYS531 3.3 65.2 1.0
C A:ASN505 3.5 51.4 1.0
CG A:ASN507 3.6 66.8 1.0
CB A:ASN505 3.8 61.6 1.0
CA A:LYS531 3.9 62.7 1.0
ND2 A:ASN507 4.1 64.9 1.0
CA A:ASN505 4.2 53.4 1.0
O A:ALA502 4.3 53.6 1.0
N A:LYS532 4.4 65.8 1.0
CB A:LYS531 4.5 55.3 1.0
N A:PRO506 4.5 53.0 1.0
N A:ASN507 4.6 58.5 1.0
C A:PRO506 4.6 57.3 1.0
CA A:LYS532 4.6 66.0 1.0
CA A:PRO506 4.7 55.4 1.0
CB A:ASN507 4.8 64.4 1.0
O A:LEU533 5.0 56.7 1.0

Calcium binding site 5 out of 9 in 1clq

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Calcium binding site 5 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


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 A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:98.0
occ:1.00
 OP1 D:DG1 2.3 59.0 1.0
OE2 A:GLU116 2.7 70.7 1.0
OE1 A:GLU116 3.1 76.4 1.0
CD A:GLU116 3.2 71.1 1.0
P D:DG1 3.5 49.1 1.0
OP2 D:DG1 3.7 60.1 1.0
OD2 A:ASP114 3.7 77.8 1.0
CA D:CA1003 4.1 73.4 1.0
OD2 A:ASP327 4.2 67.1 1.0
O5' D:DG1 4.4 54.2 1.0
O3' D:DC2 4.7 38.3 1.0
CG A:GLU116 4.7 63.7 1.0
CG A:ASP114 4.8 76.5 1.0
C5' D:DG1 4.8 55.2 1.0
C3' D:DG1 4.9 66.5 1.0
O A:ILE115 4.9 62.9 1.0

Calcium binding site 6 out of 9 in 1clq

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Calcium binding site 6 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


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 A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:58.6
occ:1.00
 OE1 A:GLU219 2.3 66.8 1.0
OD2 A:ASP275 2.3 65.0 1.0
OD1 A:ASP275 2.6 65.4 1.0
CG A:ASP275 2.8 53.9 1.0
CD A:GLU219 3.5 57.5 1.0
C5 E:DC3 4.2 75.8 1.0
O6 E:DG2 4.2 61.0 1.0
CG A:GLU219 4.2 42.7 1.0
OE2 A:GLU219 4.3 61.9 1.0
CB A:ASP275 4.4 48.5 1.0
CB A:GLU219 4.4 34.0 1.0
OG A:SER220 4.7 47.5 1.0
CB A:SER220 4.9 42.8 1.0
OD1 A:ASN217 4.9 42.5 1.0
C6 E:DC3 4.9 76.4 1.0
N4 E:DC3 5.0 78.6 1.0
N7 E:DG2 5.0 55.1 1.0

Calcium binding site 7 out of 9 in 1clq

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Calcium binding site 7 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


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 A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:94.1
occ:1.00
 OE2 A:GLU716 3.0 82.4 1.0
CD A:GLU716 4.1 76.8 1.0
CB A:ASP684 4.2 61.4 1.0
OD2 A:ASP684 4.4 85.6 1.0
CG A:GLU716 4.6 71.2 1.0
O A:ASP684 4.6 50.8 1.0
CG A:ASP684 4.8 78.0 1.0

Calcium binding site 8 out of 9 in 1clq

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Calcium binding site 8 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


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 A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:0.8
occ:1.00
 O A:ASN676 2.5 35.9 1.0
N A:ASN676 3.3 37.9 1.0
C A:ASN676 3.5 41.0 1.0
SG A:CYS671 3.5 54.6 1.0
O A:CYS671 3.7 51.0 1.0
CA A:ASN676 3.9 37.5 1.0
C A:ASN675 4.1 38.7 1.0
C A:CYS671 4.2 47.1 1.0
CA A:ASN675 4.3 38.1 1.0
NZ A:LYS465 4.4 57.4 1.0
CA A:GLU672 4.4 49.8 1.0
N A:GLU672 4.6 51.6 1.0
CB A:ASN676 4.6 33.1 1.0
N A:LYS677 4.6 41.9 1.0
OD1 A:ASN675 4.8 50.5 1.0
CB A:CYS671 4.8 39.7 1.0
O A:LYS677 4.9 41.9 1.0
C A:LYS677 4.9 40.5 1.0

Calcium binding site 9 out of 9 in 1clq

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Calcium binding site 9 out of 9 in the Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Replication Fork Dna Polymerase Editing Complex at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1025

b:82.3
occ:1.00
 OD1 A:ASP623 2.8 57.4 1.0
OG A:SER624 2.9 39.1 1.0
OD2 A:ASP621 3.0 66.5 1.0
O A:HOH1071 3.0 53.7 1.0
O A:HOH1150 3.1 52.4 1.0
CG A:ASP623 3.8 50.0 1.0
CG A:ASP621 3.9 69.5 1.0
OD2 A:ASP411 3.9 78.0 1.0
OD1 A:ASP411 4.0 79.5 1.0
OD2 A:ASP623 4.0 60.0 1.0
CG A:ASP411 4.1 71.0 1.0
CB A:SER624 4.3 29.4 1.0
OD1 A:ASP621 4.5 75.9 1.0
CB A:ASP621 4.8 66.5 1.0

Reference:

Y.Shamoo, T.A.Steitz. Building A Replisome From Interacting Pieces: Sliding Clamp Complexed to A Peptide From Dna Polymerase and A Polymerase Editing Complex. Cell(Cambridge,Mass.) V. 99 155 1999.
ISSN: ISSN 0092-8674
PubMed: 10535734
DOI: 10.1016/S0092-8674(00)81647-5
Page generated: Sat Dec 12 02:51:44 2020

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