Atomistry » Calcium » PDB 5mfd-5mnl » 5mkg
Atomistry »
  Calcium »
    PDB 5mfd-5mnl »
      5mkg »

Calcium in PDB 5mkg: PA3825-Eal Ca-Cdg Structure

Protein crystallography data

The structure of PA3825-Eal Ca-Cdg Structure, PDB code: 5mkg was solved by S.Horrell, D.Bellini, R.Strange, A.Wagner, M.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.29 / 2.44
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.230, 59.400, 92.780, 90.00, 115.03, 90.00
R / Rfree (%) 23.8 / 28.5

Calcium Binding Sites:

The binding sites of Calcium atom in the PA3825-Eal Ca-Cdg Structure (pdb code 5mkg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the PA3825-Eal Ca-Cdg Structure, PDB code: 5mkg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5mkg

Go back to Calcium Binding Sites List in 5mkg
Calcium binding site 1 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of PA3825-Eal Ca-Cdg Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:98.0
occ:1.00
O A:HOH426 2.8 53.8 1.0
OE2 A:GLU135 2.9 90.0 0.7
O A:ILE99 3.2 63.2 1.0
OE1 A:GLU135 3.4 87.9 0.7
CD A:GLU135 3.6 88.7 0.7
N21 A:C2E304 3.8 49.8 1.0
C A:ILE99 4.1 60.4 1.0
N31 A:C2E304 4.1 46.1 1.0
C21 A:C2E304 4.3 47.9 1.0
N A:ILE99 4.3 56.2 1.0
O2A A:C2E304 4.4 44.6 1.0
OE2 A:GLU62 4.4 73.0 1.0
CB A:ASN98 4.5 50.5 1.0
CG2 A:THR132 4.6 60.3 1.0
O A:HOH419 4.6 68.3 1.0
O A:GLU130 4.8 46.4 1.0
N A:SER100 4.8 62.3 1.0
C A:ASN98 4.8 52.5 1.0
CA A:SER100 4.8 66.7 1.0
CA A:ILE99 4.9 60.0 1.0
CA A:ASN98 5.0 50.4 1.0

Calcium binding site 2 out of 7 in 5mkg

Go back to Calcium Binding Sites List in 5mkg
Calcium binding site 2 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of PA3825-Eal Ca-Cdg Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:98.1
occ:1.00
OD1 A:ASP161 2.2 62.2 1.0
O1P A:C2E304 2.8 52.7 1.0
OE1 A:GLU217 2.8 48.4 1.0
O A:HOH421 2.8 61.1 1.0
OD1 A:ASP183 2.9 53.5 1.0
CG A:ASP161 3.3 67.0 1.0
CD A:GLU217 3.5 46.7 1.0
OE2 A:GLU217 3.7 48.3 0.7
O5' A:C2E304 3.8 49.5 1.0
OD2 A:ASP161 3.9 69.7 1.0
CG A:ASP183 4.0 54.0 1.0
P1 A:C2E304 4.0 49.7 1.0
OE1 A:GLN184 4.0 65.1 0.8
N A:GLN184 4.3 51.1 0.8
CB A:ASP161 4.4 64.7 1.0
CA A:ASP183 4.4 50.1 1.0
OD1 A:ASP160 4.4 65.5 1.0
CD A:GLN184 4.4 63.1 0.8
CA A:ASP161 4.5 63.7 1.0
CB A:ASP183 4.6 51.9 1.0
O A:HOH405 4.7 36.9 1.0
CB A:GLU217 4.7 39.1 1.0
CG A:GLU217 4.7 43.1 1.0
N A:ASP161 4.8 60.3 1.0
O3A A:C2E304 4.8 47.2 1.0
OD2 A:ASP183 4.8 54.7 1.0
CB A:GLN184 4.9 55.4 0.8
C A:ASP183 4.9 50.5 1.0
CG A:GLN184 4.9 59.0 0.8

Calcium binding site 3 out of 7 in 5mkg

Go back to Calcium Binding Sites List in 5mkg
Calcium binding site 3 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of PA3825-Eal Ca-Cdg Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:51.8
occ:1.00
O2P A:C2E304 2.2 46.8 1.0
OE2 A:GLU39 2.3 43.6 1.0
OD2 A:ASP160 2.3 62.3 1.0
OE1 A:GLU130 2.4 50.6 1.0
OD1 A:ASN98 2.4 50.7 1.0
O A:HOH405 2.5 36.9 1.0
CG A:ASP160 3.1 60.3 1.0
OD1 A:ASP160 3.2 65.5 1.0
CD A:GLU39 3.3 45.8 1.0
P1 A:C2E304 3.3 49.7 1.0
CG A:ASN98 3.4 49.7 1.0
CD A:GLU130 3.6 49.7 1.0
O1P A:C2E304 3.6 52.7 1.0
OE1 A:GLU39 3.7 44.1 1.0
ND2 A:ASN98 3.8 48.2 1.0
O5' A:C2E304 4.1 49.5 1.0
NZ A:LYS181 4.3 48.8 1.0
OE2 A:GLU130 4.3 48.7 1.0
CB A:GLU130 4.5 49.0 1.0
CB A:ASP160 4.5 56.7 1.0
CG A:GLU130 4.5 50.3 1.0
CG A:GLU39 4.6 45.3 1.0
O3A A:C2E304 4.6 47.2 1.0
C5' A:C2E304 4.7 47.7 1.0
OE1 A:GLU217 4.7 48.4 1.0
CB A:ASN98 4.8 50.5 1.0
O A:HOH426 4.8 53.8 1.0
C2A A:C2E304 4.9 46.8 1.0

Calcium binding site 4 out of 7 in 5mkg

Go back to Calcium Binding Sites List in 5mkg
Calcium binding site 4 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of PA3825-Eal Ca-Cdg Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:95.4
occ:1.00
O B:HOH423 2.6 45.0 1.0
OE2 B:GLU135 3.0 85.7 0.7
O B:ILE99 3.1 60.3 1.0
OE1 B:GLU135 3.6 85.1 0.7
CD B:GLU135 3.7 85.8 0.7
C B:ILE99 3.9 59.7 1.0
OE2 B:GLU62 4.3 68.0 1.0
CA B:SER100 4.4 67.9 1.0
N2 B:C2E304 4.5 42.5 1.0
N B:SER100 4.5 63.8 1.0
O B:GLU130 4.5 40.8 1.0
N B:ILE99 4.5 52.6 1.0
CG2 B:THR132 4.6 59.3 1.0
N B:THR132 4.7 53.4 1.0
O2' B:C2E304 4.9 40.4 1.0
CA B:ILE99 4.9 56.3 1.0
N3 B:C2E304 4.9 40.9 1.0
OG1 B:THR132 5.0 57.7 1.0
CB B:ASN98 5.0 46.2 1.0

Calcium binding site 5 out of 7 in 5mkg

Go back to Calcium Binding Sites List in 5mkg
Calcium binding site 5 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of PA3825-Eal Ca-Cdg Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:38.9
occ:1.00
O21 B:C2E304 2.2 43.1 1.0
OD2 B:ASP160 2.3 50.1 1.0
OE2 B:GLU39 2.3 38.3 1.0
OE1 B:GLU130 2.3 41.4 1.0
OD1 B:ASN98 2.4 42.8 1.0
O B:HOH408 2.4 35.5 1.0
CG B:ASP160 3.1 50.2 1.0
OD1 B:ASP160 3.2 52.0 1.0
CD B:GLU39 3.3 38.3 1.0
CG B:ASN98 3.4 44.5 1.0
P11 B:C2E304 3.5 42.0 1.0
CD B:GLU130 3.5 40.9 1.0
CA B:CA303 3.6 0.1 1.0
OE1 B:GLU39 3.7 37.8 1.0
ND2 B:ASN98 3.8 40.3 1.0
O11 B:C2E304 4.0 49.9 1.0
O5A B:C2E304 4.2 43.6 1.0
NZ B:LYS181 4.2 39.2 1.0
OE2 B:GLU130 4.3 40.2 1.0
CB B:GLU130 4.3 40.0 1.0
CB B:ASP160 4.4 49.4 1.0
CG B:GLU130 4.5 40.3 1.0
OE2 B:GLU217 4.5 43.4 0.7
CG B:GLU39 4.6 36.6 1.0
C5A B:C2E304 4.7 42.8 1.0
O B:HOH423 4.7 45.0 1.0
O3' B:C2E304 4.7 40.1 1.0
CB B:ASN98 4.7 46.2 1.0
C2' B:C2E304 5.0 40.7 1.0

Calcium binding site 6 out of 7 in 5mkg

Go back to Calcium Binding Sites List in 5mkg
Calcium binding site 6 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of PA3825-Eal Ca-Cdg Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:0.1
occ:1.00
O11 B:C2E304 2.3 49.9 1.0
OE1 B:GLU217 2.4 43.5 0.7
OD1 B:ASP161 2.4 61.6 1.0
OD1 B:ASP160 2.4 52.0 1.0
O B:HOH408 2.8 35.5 1.0
OE2 B:GLU217 2.9 43.4 0.7
CD B:GLU217 3.0 40.8 0.7
P11 B:C2E304 3.0 42.0 1.0
O5A B:C2E304 3.1 43.6 1.0
CG B:ASP160 3.4 50.2 1.0
O21 B:C2E304 3.4 43.1 1.0
CG B:ASP161 3.5 63.6 1.0
CA B:CA302 3.6 38.9 1.0
OD2 B:ASP160 3.7 50.1 1.0
OD2 B:ASP161 4.0 67.9 1.0
N B:ASP161 4.1 53.8 1.0
C5A B:C2E304 4.3 42.8 1.0
CG B:GLU217 4.4 36.8 0.7
O3' B:C2E304 4.5 40.1 1.0
CA B:ASP161 4.6 58.2 1.0
CB B:ASP161 4.6 60.7 1.0
CB B:ASP160 4.7 49.4 1.0
OD1 B:ASP183 4.9 53.9 1.0
C B:ASP160 5.0 51.1 1.0

Calcium binding site 7 out of 7 in 5mkg

Go back to Calcium Binding Sites List in 5mkg
Calcium binding site 7 out of 7 in the PA3825-Eal Ca-Cdg Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of PA3825-Eal Ca-Cdg Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:56.8
occ:1.00
O B:HOH410 2.5 34.0 1.0
O B:HOH429 2.6 41.9 1.0
O B:HOH431 2.8 54.5 1.0
OD2 B:ASP234 2.8 48.2 1.0
OD1 B:ASP234 2.9 50.6 1.0
O B:HOH424 2.9 59.0 1.0
CG B:ASP234 3.2 47.5 1.0
O B:GLY232 4.3 44.0 1.0
O B:LEU212 4.5 41.9 1.0
CB B:ASP234 4.7 45.5 1.0
OD1 B:ASP213 5.0 37.2 0.7

Reference:

D.Bellini, S.Horrell, A.Hutchin, C.W.Phippen, R.W.Strange, Y.Cai, A.Wagner, J.S.Webb, I.Tews, M.A.Walsh. Dimerisation Induced Formation of the Active Site and the Identification of Three Metal Sites in Eal-Phosphodiesterases. Sci Rep V. 7 42166 2017.
ISSN: ESSN 2045-2322
PubMed: 28186120
DOI: 10.1038/SREP42166
Page generated: Sat Dec 12 05:38:03 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy