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Calcium in PDB 4pnv: E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions

Enzymatic activity of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions

All present enzymatic activity of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions:
2.7.7.7;

Protein crystallography data

The structure of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions, PDB code: 4pnv was solved by Z.Yin, A.J.Oakley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.55 / 1.86
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.138, 70.257, 84.469, 90.00, 114.67, 90.00
R / Rfree (%) 18.3 / 23.4

Other elements in 4pnv:

The structure of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions (pdb code 4pnv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions, PDB code: 4pnv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4pnv

Go back to Calcium Binding Sites List in 4pnv
Calcium binding site 1 out of 8 in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:14.7
occ:1.00
 OD1 A:ASN118 2.2 18.2 1.0
O A:HOH643 2.3 16.0 1.0
O A:LEU119 2.3 18.0 1.0
O A:HOH543 2.4 21.6 1.0
O A:HOH542 2.5 18.4 1.0
O A:HOH581 2.5 14.7 1.0
O A:HOH520 2.6 14.7 1.0
CG A:ASN118 3.5 19.4 1.0
C A:LEU119 3.5 19.3 1.0
N A:LEU119 3.7 20.0 1.0
CA A:LEU119 4.1 20.4 1.0
C A:ASN118 4.2 20.7 1.0
O A:HOH888 4.2 22.2 1.0
OD1 A:ASP121 4.2 17.6 1.0
ND2 A:ASN118 4.2 20.4 1.0
O A:HOH837 4.3 33.0 1.0
O A:HOH519 4.4 17.0 1.0
CA A:ASN118 4.5 20.0 1.0
CB A:LEU119 4.5 21.5 1.0
CB A:ASN118 4.5 19.8 1.0
N A:ASP120 4.6 19.6 1.0
OE2 A:GLU52 4.6 16.3 1.0
C A:ASP120 4.6 18.3 1.0
O A:HOH629 4.7 20.8 1.0
OE1 A:GLU52 4.7 15.1 1.0
N A:ASP121 4.8 17.3 1.0
O A:ASP120 4.8 17.8 1.0
O A:ASN118 4.8 20.5 1.0
CA A:ASP120 4.9 19.2 1.0

Calcium binding site 2 out of 8 in 4pnv

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Calcium binding site 2 out of 8 in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:62.2
occ:1.00
 O A:ARG103 2.7 17.0 1.0
OE2 B:GLU303 2.8 18.3 1.0
C A:ARG103 3.2 18.1 1.0
CD A:ARG105 3.3 26.1 1.0
CD1 B:ILE305 3.6 18.8 1.0
CG1 B:ILE305 3.6 17.8 1.0
CA A:ARG103 3.7 18.9 1.0
CD B:GLU303 3.7 17.8 1.0
CG B:GLU303 3.9 17.4 1.0
CB A:ARG103 3.9 20.2 1.0
O B:GLU303 4.0 14.7 1.0
N B:ILE305 4.0 15.2 1.0
NE A:ARG105 4.1 29.2 1.0
N A:SER104 4.2 17.4 1.0
CB B:ILE305 4.2 17.1 1.0
C B:GLU303 4.4 14.2 1.0
CG A:ARG105 4.4 23.1 1.0
C B:GLU304 4.5 14.0 1.0
CB B:GLU303 4.5 16.1 1.0
CA B:GLU304 4.6 13.2 1.0
CA A:SER104 4.6 16.7 1.0
N A:ARG105 4.6 16.6 1.0
N B:GLU304 4.7 13.3 1.0
O B:HOH900 4.7 35.0 1.0
CG A:ARG103 4.7 22.0 1.0
CA B:ILE305 4.8 16.4 1.0
CB A:ARG105 4.8 19.9 1.0
C A:SER104 4.8 16.8 1.0
OE1 B:GLU303 4.8 18.4 1.0

Calcium binding site 3 out of 8 in 4pnv

Go back to Calcium Binding Sites List in 4pnv
Calcium binding site 3 out of 8 in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:67.4
occ:1.00
 O A:HOH746 2.6 35.0 1.0
O A:HOH515 2.7 25.3 1.0
O A:TYR153 2.8 28.6 1.0
O A:HOH641 3.5 26.0 1.0
CG2 A:VAL237 3.6 24.2 1.0
C A:TYR153 3.7 30.9 1.0
N A:GLY157 3.9 18.9 1.0
CG1 A:VAL237 3.9 24.8 1.0
CB A:ASN156 3.9 22.2 1.0
CA A:PRO196 4.0 17.1 1.0
CB A:PRO196 4.0 16.9 1.0
C A:ASN156 4.1 20.2 1.0
CB A:TYR153 4.3 31.8 0.5
CA A:GLY157 4.3 18.4 1.0
CB A:TYR153 4.3 33.5 0.5
CA A:TYR153 4.4 32.0 0.5
CA A:TYR153 4.4 32.8 0.5
CB A:VAL237 4.4 24.4 1.0
CA A:ASN156 4.4 21.5 1.0
O A:ASN156 4.6 19.1 1.0
N A:ARG197 4.6 19.0 1.0
N A:TYR154 4.6 29.9 1.0
N A:ASN156 4.7 21.6 1.0
CA A:TYR154 4.8 29.8 1.0
O A:HOH925 4.8 36.6 1.0
C A:PRO196 4.9 17.7 1.0
ND2 A:ASN156 5.0 23.2 1.0
O A:HOH570 5.0 17.8 1.0
CG A:ASN156 5.0 23.3 1.0
O A:HOH915 5.0 32.7 1.0

Calcium binding site 4 out of 8 in 4pnv

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Calcium binding site 4 out of 8 in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:49.8
occ:1.00
 O A:HOH893 2.4 26.4 1.0
O A:HOH889 2.5 21.8 1.0
O A:HIS255 2.8 19.8 1.0
N A:SER311 3.0 20.2 1.0
O A:HOH745 3.1 28.0 1.0
OG A:SER311 3.2 22.0 1.0
O A:HOH615 3.3 21.9 1.0
N A:GLY312 3.5 23.0 1.0
CE1 A:HIS255 3.6 27.1 1.0
NE2 A:HIS255 3.7 27.0 1.0
ND1 A:HIS255 3.7 26.4 1.0
CD1 A:TYR310 3.8 18.3 1.0
CA A:SER311 3.8 21.5 1.0
CA A:TYR310 3.9 18.0 1.0
C A:HIS255 3.9 20.5 1.0
C A:SER311 3.9 22.6 1.0
CD2 A:HIS255 3.9 26.9 1.0
C A:TYR310 3.9 18.4 1.0
CG A:HIS255 4.0 25.5 1.0
CB A:SER311 4.1 21.8 1.0
N A:HIS255 4.1 22.7 1.0
CE1 A:TYR310 4.2 18.7 1.0
CA A:GLY312 4.4 22.7 1.0
CG A:TYR310 4.4 17.9 1.0
CA A:HIS255 4.5 22.2 1.0
CB A:TYR310 4.8 17.8 1.0
O A:SER311 4.8 24.4 1.0
CB A:HIS255 4.8 23.5 1.0
N A:TYR310 4.9 17.5 1.0
O A:HOH826 5.0 35.0 1.0

Calcium binding site 5 out of 8 in 4pnv

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Calcium binding site 5 out of 8 in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:65.5
occ:1.00
 O A:HOH725 2.4 25.8 1.0
O A:LEU14 2.7 16.9 1.0
CA A:SER18 3.3 28.7 1.0
CB A:SER18 3.5 29.8 1.0
N A:SER18 3.6 24.6 1.0
CD1 A:LEU33 3.6 13.9 0.5
C A:LEU14 3.7 16.8 1.0
O A:HOH868 4.0 33.9 1.0
CG A:LEU33 4.1 13.8 0.5
CD2 A:LEU33 4.1 13.8 0.5
C A:VAL17 4.1 21.4 1.0
CG2 A:VAL17 4.1 20.3 1.0
CA A:LEU14 4.3 16.0 1.0
O A:ALA72 4.3 13.5 1.0
CB A:ALA72 4.4 14.3 1.0
O A:VAL17 4.5 20.7 1.0
CB A:PHE76 4.5 14.4 1.0
CB A:LEU14 4.5 15.6 1.0
O A:HOH920 4.5 36.3 1.0
C A:SER18 4.7 30.6 1.0
OG A:SER18 4.7 31.5 1.0
C A:ALA72 4.7 13.9 1.0
N A:GLN15 4.7 17.9 1.0
CD2 A:LEU14 4.8 15.8 1.0
CA A:ALA72 4.9 13.8 1.0
CG A:PHE76 5.0 16.2 1.0

Calcium binding site 6 out of 8 in 4pnv

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Calcium binding site 6 out of 8 in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:14.6
occ:1.00
 O B:HOH661 2.2 16.2 1.0
O B:HOH557 2.3 11.4 1.0
O B:LEU119 2.3 16.3 1.0
OD1 B:ASN118 2.4 14.5 1.0
O B:HOH522 2.4 13.2 1.0
O B:HOH596 2.5 18.6 1.0
O B:HOH520 2.6 11.3 1.0
C B:LEU119 3.5 16.4 1.0
CG B:ASN118 3.5 15.5 1.0
N B:LEU119 3.7 17.0 1.0
CA B:LEU119 4.0 17.3 1.0
OD1 B:ASP121 4.2 17.4 1.0
C B:ASN118 4.2 16.4 1.0
O B:HOH570 4.2 14.6 1.0
ND2 B:ASN118 4.3 15.3 1.0
O B:HOH746 4.3 38.6 1.0
CB B:LEU119 4.3 18.2 1.0
N B:ASP120 4.6 16.1 1.0
CA B:ASN118 4.6 16.0 1.0
CB B:ASN118 4.7 15.7 1.0
C B:ASP120 4.7 16.6 1.0
OE1 B:GLU52 4.7 15.1 1.0
OE2 B:GLU52 4.8 15.5 1.0
O B:HOH648 4.8 17.8 1.0
N B:ASP121 4.8 16.3 1.0
O B:ASP120 4.8 15.9 1.0
O B:HOH826 4.8 30.8 1.0
O B:ASN118 4.9 16.9 1.0
CA B:ASP120 5.0 16.8 1.0

Calcium binding site 7 out of 8 in 4pnv

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Calcium binding site 7 out of 8 in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:45.2
occ:1.00
 O B:THR4 2.5 16.9 1.0
O B:HOH642 2.8 27.3 1.0
O B:HOH503 3.0 16.4 1.0
N B:GLN61 3.1 28.2 1.0
N B:VAL60 3.3 24.0 1.0
CB B:GLN61 3.4 27.2 1.0
CG B:GLN61 3.5 27.8 1.0
CA B:LEU59 3.6 21.2 1.0
C B:THR4 3.6 16.6 1.0
CG2 B:VAL5 3.6 19.9 1.0
C B:LEU59 3.7 22.2 1.0
CA B:GLN61 3.7 27.0 1.0
CB B:LEU59 3.8 20.0 1.0
CD2 B:LEU59 3.9 19.3 1.0
O B:GLN61 4.0 24.9 1.0
C B:VAL60 4.1 28.1 1.0
O B:HOH504 4.1 12.3 1.0
CA B:VAL5 4.1 18.5 1.0
CA B:VAL60 4.2 27.0 1.0
C B:GLN61 4.2 26.1 1.0
N B:VAL5 4.3 17.4 1.0
CD B:GLN61 4.3 28.5 1.0
CG2 B:VAL60 4.4 28.4 1.0
CB B:VAL5 4.5 19.5 1.0
NE2 B:GLN61 4.5 28.8 1.0
CG B:LEU59 4.5 19.6 1.0
N B:THR4 4.6 15.3 1.0
CA B:THR4 4.7 16.3 1.0
O B:LEU59 4.7 20.9 1.0
O B:ALA58 4.8 22.2 1.0
N B:LEU59 4.9 21.2 1.0
CB B:VAL60 4.9 28.4 1.0

Calcium binding site 8 out of 8 in 4pnv

Go back to Calcium Binding Sites List in 4pnv
Calcium binding site 8 out of 8 in the E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of E. Coli Sliding Clamp Apo-Crystal in P21 Space Group with Larger Cell Dimensions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:40.0
occ:1.00
 OG1 B:THR110 2.6 15.9 1.0
O B:HOH911 2.8 32.9 1.0
O B:HOH507 2.8 17.4 1.0
CB B:THR110 3.3 15.4 1.0
N B:PRO112 3.3 15.8 1.0
C B:LEU111 3.4 15.2 1.0
C B:THR110 3.5 15.5 1.0
O B:THR110 3.5 15.9 1.0
CD B:PRO112 3.6 15.9 1.0
CA B:LEU111 3.6 15.3 1.0
N B:LEU111 3.6 15.3 1.0
O B:HOH853 3.7 38.1 1.0
CA B:PRO112 3.8 15.2 1.0
O B:LEU111 3.8 13.9 1.0
CG B:PRO112 3.8 15.9 1.0
CA B:THR110 4.1 14.9 1.0
O B:HOH688 4.1 19.8 1.0
OE1 B:GLU95 4.3 35.4 1.0
O B:GLY94 4.4 22.5 1.0
CB B:PRO112 4.4 15.6 1.0
OG1 B:THR68 4.4 12.9 1.0
OE2 B:GLU95 4.4 36.2 1.0
CD B:GLU95 4.6 31.6 1.0
CG2 B:THR110 4.6 15.5 1.0
CA B:GLU95 4.8 22.9 1.0
O B:HOH543 4.9 12.4 1.0
N B:THR110 5.0 14.5 1.0

Reference:

Z.Yin, A.J.Oakley. Reaching Beyond the Anchor Site: Inhibitor Design Mimicking the Mechanism of Linear Motif Recognition By the E. Coli Sliding Clamp To Be Published.
Page generated: Sun Jul 14 12:09:32 2024

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