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Calcium in PDB 4mlz: Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans

Protein crystallography data

The structure of Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans, PDB code: 4mlz was solved by C.Chang, G.Chhor, M.Endres, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.80 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.678, 72.741, 71.306, 90.00, 101.32, 90.00
R / Rfree (%) 13.5 / 19.3

Other elements in 4mlz:

The structure of Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans also contains other interesting chemical elements:

Potassium (K) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans (pdb code 4mlz). 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 Periplasmic Binding Protein From Jonesia Denitrificans, PDB code: 4mlz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4mlz

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Calcium binding site 1 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:20.2
occ:1.00
 O A:HOH626 2.3 26.6 1.0
O A:HOH573 2.4 20.3 1.0
OD1 A:ASP161 2.5 16.3 1.0
O A:HOH535 2.5 18.1 1.0
OD2 A:ASP161 2.5 18.0 1.0
O A:HOH581 2.6 17.4 1.0
O A:HOH520 2.6 19.8 1.0
CG A:ASP161 2.9 18.0 1.0
O A:HOH602 4.1 23.2 1.0
CA A:CA402 4.3 16.8 1.0
O A:HOH578 4.3 17.5 1.0
OD2 A:ASP163 4.3 17.7 1.0
CB A:ASP161 4.4 15.1 1.0
CG A:ASP163 4.8 15.4 1.0
N A:ARG162 4.8 12.7 1.0
O A:HOH663 5.0 39.9 1.0
OD1 A:ASP163 5.0 16.3 1.0

Calcium binding site 2 out of 9 in 4mlz

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Calcium binding site 2 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.8
occ:1.00
 OD2 A:ASP161 2.3 18.0 1.0
OD2 A:ASP163 2.4 17.7 1.0
O A:HOH592 2.5 18.3 1.0
OD1 A:ASP163 2.7 16.3 1.0
CG A:ASP163 2.9 15.4 1.0
CG A:ASP161 3.4 18.0 1.0
CB A:ASP161 3.9 15.1 1.0
O A:HOH581 4.1 17.4 1.0
O A:HOH528 4.2 16.4 1.0
O A:HOH520 4.2 19.8 1.0
CA A:CA401 4.3 20.2 1.0
CB A:ASP163 4.4 13.1 1.0
OD1 A:ASP161 4.5 16.3 1.0
O A:HOH632 4.9 23.1 1.0

Calcium binding site 3 out of 9 in 4mlz

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Calcium binding site 3 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:21.2
occ:1.00
 O A:HOH657 2.3 21.6 1.0
O A:ASP98 2.4 13.9 1.0
O A:HOH622 2.4 30.4 1.0
O A:HOH580 2.4 22.5 1.0
O A:HOH667 2.4 21.9 1.0
O A:HOH569 2.4 19.5 1.0
O A:HOH566 2.6 27.3 1.0
C A:ASP98 3.6 11.9 1.0
O A:HOH661 4.1 30.1 1.0
CA A:ASP98 4.3 13.1 1.0
O A:HOH702 4.5 31.7 1.0
O A:HOH690 4.5 24.9 1.0
CB A:ASP98 4.5 15.3 1.0
N A:ARG99 4.5 11.2 1.0
O A:GLU78 4.7 12.8 1.0
CA A:ARG99 4.7 11.2 1.0
OD2 A:ASP98 4.7 26.2 1.0
O A:HOH558 4.7 15.7 1.0
CG1 A:VAL101 5.0 14.0 1.0

Calcium binding site 4 out of 9 in 4mlz

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Calcium binding site 4 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:27.7
occ:1.00
 OE2 A:GLU220 2.3 21.6 1.0
O A:HOH744 2.3 30.4 1.0
O A:HOH645 2.4 23.6 1.0
O A:HOH654 2.4 25.6 1.0
O A:HOH601 2.5 20.9 1.0
OE1 A:GLU220 2.8 18.0 1.0
CD A:GLU220 2.9 18.0 1.0
CG A:GLU220 4.4 16.0 1.0
O A:HOH545 4.8 21.6 1.0

Calcium binding site 5 out of 9 in 4mlz

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Calcium binding site 5 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:14.8
occ:1.00
 OD2 B:ASP161 2.4 15.8 1.0
OD2 B:ASP163 2.4 14.0 1.0
O B:HOH531 2.4 13.9 1.0
OD1 B:ASP163 2.6 13.7 1.0
CG B:ASP163 2.9 13.4 1.0
CG B:ASP161 3.4 15.1 1.0
CB B:ASP161 3.9 12.5 1.0
O B:HOH547 4.1 13.5 1.0
CB B:ASP163 4.4 12.3 1.0
OD1 B:ASP161 4.5 14.8 1.0
O B:HOH728 5.0 21.6 1.0

Calcium binding site 6 out of 9 in 4mlz

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Calcium binding site 6 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:18.7
occ:1.00
 O B:HOH598 2.4 22.0 1.0
OD2 B:ASP116 2.4 18.2 1.0
O B:HOH574 2.5 16.1 1.0
O B:HOH542 2.5 21.8 1.0
O B:HOH568 2.5 17.6 1.0
O B:HOH613 2.5 17.8 1.0
CG B:ASP116 3.5 17.4 1.0
OD1 B:ASP116 4.0 16.7 1.0
O B:HOH789 4.3 33.3 1.0
OE2 B:GLU117 4.5 14.4 1.0
CB B:ASP116 4.6 15.9 1.0

Calcium binding site 7 out of 9 in 4mlz

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Calcium binding site 7 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:29.6
occ:1.00
 O B:HOH699 2.3 27.9 1.0
O B:ALA223 2.4 20.1 1.0
O B:HOH754 2.4 26.2 1.0
O B:HOH757 2.4 29.8 1.0
O B:HOH795 2.5 41.5 1.0
O B:ILE225 2.6 33.9 1.0
C B:ILE225 3.6 28.4 1.0
C B:ALA223 3.6 16.0 1.0
C B:ALA224 4.0 20.8 1.0
N B:ILE225 4.1 20.7 1.0
O B:ALA224 4.2 22.2 1.0
CA B:ALA224 4.3 19.2 1.0
O B:HOH745 4.3 36.4 1.0
O B:HOH776 4.3 31.5 1.0
N B:SER226 4.3 30.1 1.0
N B:ALA224 4.4 15.3 1.0
CA B:ILE225 4.4 23.4 1.0
CA B:SER226 4.5 32.8 1.0
CA B:ALA223 4.6 17.5 1.0
CD B:PRO227 4.6 33.2 1.0
O B:HOH659 4.8 29.1 1.0
O B:LEU222 5.0 18.5 1.0

Calcium binding site 8 out of 9 in 4mlz

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Calcium binding site 8 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:22.3
occ:1.00
 O B:HOH765 2.3 21.5 1.0
OE2 B:GLU220 2.3 20.6 1.0
O B:HOH616 2.3 21.1 1.0
O B:HOH608 2.4 23.8 1.0
O B:HOH615 2.5 19.1 1.0
OE1 B:GLU220 2.6 16.6 1.0
CD B:GLU220 2.8 16.2 1.0
CG B:GLU220 4.3 13.5 1.0
O B:HOH592 4.7 20.2 1.0
O B:HOH544 4.7 21.7 1.0
O B:HOH742 4.8 31.3 1.0

Calcium binding site 9 out of 9 in 4mlz

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Calcium binding site 9 out of 9 in the Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans


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 Periplasmic Binding Protein From Jonesia Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:38.3
occ:1.00
 O B:HOH800 2.2 42.6 1.0
O B:HOH735 2.3 42.3 1.0
O B:HOH590 2.3 26.7 1.0
O B:HOH564 2.3 25.6 1.0
O B:ASP98 2.7 18.5 1.0
O B:HOH695 2.8 25.5 1.0
C B:ASP98 3.9 15.3 1.0
O B:HOH599 4.3 27.3 1.0
O B:HOH640 4.4 20.8 1.0
CA B:ASP98 4.7 16.5 1.0
O B:GLU78 4.7 13.1 1.0
N B:ARG99 4.8 13.6 1.0
O B:HOH540 4.8 16.1 1.0
CG1 B:VAL101 4.9 16.8 1.0
CA B:ARG99 4.9 13.1 1.0
CB B:ASP98 4.9 19.5 1.0

Reference:

C.Chang, G.Chhor, M.Endres, A.Joachimiak. Crystal Structure of Periplasmic Binding Protein From Jonesia Denitrificans To Be Published.
Page generated: Wed Jul 9 00:26:25 2025

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