Atomistry » Calcium » PDB 4pkg-4q1l » 4pnv
Atomistry »
  Calcium »
    PDB 4pkg-4q1l »
      4pnv »

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

Go back to Calcium Binding Sites List in 4pnv
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

Go back to Calcium Binding Sites List in 4pnv
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

Go back to Calcium Binding Sites List in 4pnv
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

Go back to Calcium Binding Sites List in 4pnv
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

Go back to Calcium Binding Sites List in 4pnv
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

Last articles

Br in 1L0Z
Br in 1M9R
Br in 1M69
Br in 1M66
Br in 1M67
Br in 1LZ9
Br in 1M5D
Br in 1M5C
Br in 1L1G
Br in 1LWW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy