Atomistry » Calcium » PDB 5dzv-5egi » 5e7c
Atomistry »
  Calcium »
    PDB 5dzv-5egi »
      5e7c »

Calcium in PDB 5e7c: Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data

Enzymatic activity of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data

All present enzymatic activity of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data:
1.10.3.9;

Protein crystallography data

The structure of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data, PDB code: 5e7c was solved by K.Ayyer, O.Yefanov, D.Oberthuer, S.Roy-Chowdhury, L.Galli, V.Mariani, S.Basu, J.Coe, C.E.Conrad, R.Fromme, A.Schaffner, K.Doerner, D.James, C.Kupitz, M.Metz, G.Nelson, P.L.Xavier, K.R.Beyerlein, M.Schmidt, I.Sarrou, J.C.H.Spence, U.Weierstall, T.A.White, J.-H.Yang, Y.Zhao, M.Liang, A.Aquila, M.S.Hunter, J.S.Robinson, J.E.Koglin, S.Boutet, P.Fromme, A.Barty, H.N.Chapman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 4.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 133.250, 226.260, 307.090, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 27.5

Other elements in 5e7c:

The structure of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data also contains other interesting chemical elements:

Magnesium (Mg) 74 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data (pdb code 5e7c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data, PDB code: 5e7c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5e7c

Go back to Calcium Binding Sites List in 5e7c
Calcium binding site 1 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:65.3
occ:1.00
 CA1 A:OEX601 0.0 65.3 1.0
O1 A:OEX601 2.3 63.2 1.0
O2 A:OEX601 2.5 66.0 1.0
O5 A:OEX601 2.5 64.9 1.0
OD1 A:ASP170 2.9 64.6 1.0
O A:ALA344 2.9 66.4 1.0
OD2 A:ASP170 3.2 63.9 1.0
CG A:ASP170 3.3 63.3 1.0
MN2 A:OEX601 3.4 63.6 1.0
MN3 A:OEX601 3.4 64.2 1.0
MN1 A:OEX601 3.5 63.4 1.0
OE1 A:GLU189 3.6 67.1 1.0
MN4 A:OEX601 3.8 67.0 1.0
C A:ALA344 3.8 65.8 1.0
OXT A:ALA344 3.8 65.8 1.0
NH1 C:ARG357 3.8 67.2 1.0
O3 A:OEX601 3.9 64.0 1.0
OE2 A:GLU189 4.0 65.9 1.0
O4 A:OEX601 4.0 67.4 1.0
CD A:GLU189 4.1 65.3 1.0
NH2 C:ARG357 4.1 64.7 1.0
CZ C:ARG357 4.5 68.2 1.0
OH A:TYR161 4.6 63.2 1.0
CB A:ASP170 4.7 62.4 1.0
OE1 A:GLN165 4.8 64.6 1.0
CB A:GLN165 4.9 63.0 1.0
CG A:GLN165 5.0 62.6 1.0

Calcium binding site 2 out of 8 in 5e7c

Go back to Calcium Binding Sites List in 5e7c
Calcium binding site 2 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:0.1
occ:1.00
 OE1 O:GLU181 3.6 88.2 1.0
OD1 B:ASN438 3.7 69.9 1.0
OE2 B:GLU435 4.0 74.5 0.6
OE2 O:GLU181 4.1 86.9 1.0
CD O:GLU181 4.2 85.8 1.0
O B:SER439 4.4 63.4 1.0
CD B:GLU435 4.8 72.1 0.6
CG B:ASN438 4.9 67.9 1.0
OE1 B:GLU435 4.9 73.2 0.6
O B:THR434 5.0 65.9 1.0

Calcium binding site 3 out of 8 in 5e7c

Go back to Calcium Binding Sites List in 5e7c
Calcium binding site 3 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:97.3
occ:1.00
 OE1 V:GLU23 3.4 86.4 1.0
O F:ARG45 3.4 71.3 1.0
OXT F:ARG45 3.5 71.5 1.0
CD V:GLU23 3.9 84.8 1.0
OE2 V:GLU23 3.9 87.2 1.0
C F:ARG45 3.9 71.8 1.0
O A:ALA309 4.5 69.2 1.0
CB A:ALA309 5.0 67.7 1.0

Calcium binding site 4 out of 8 in 5e7c

Go back to Calcium Binding Sites List in 5e7c
Calcium binding site 4 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:90.0
occ:1.00
 O O:THR138 2.5 84.4 1.0
OD1 O:ASN200 3.2 82.6 1.0
O O:VAL201 3.4 80.2 1.0
C O:THR138 3.7 84.4 1.0
CG O:ASN200 4.1 81.4 1.0
CA O:SER139 4.1 84.3 1.0
ND2 O:ASN200 4.3 83.5 1.0
N O:SER139 4.4 84.3 1.0
C O:VAL201 4.6 79.8 1.0
C O:SER139 4.7 84.0 1.0
CA O:THR138 4.8 84.4 1.0

Calcium binding site 5 out of 8 in 5e7c

Go back to Calcium Binding Sites List in 5e7c
Calcium binding site 5 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca601

b:86.0
occ:1.00
 CA1 a:OEX601 0.0 86.0 1.0
O1 a:OEX601 2.3 83.9 1.0
O2 a:OEX601 2.5 86.6 1.0
O5 a:OEX601 2.5 85.5 1.0
OD1 a:ASP170 2.9 85.3 1.0
O a:ALA344 3.0 87.1 1.0
OD2 a:ASP170 3.1 84.5 1.0
CG a:ASP170 3.3 84.0 1.0
MN2 a:OEX601 3.4 84.3 1.0
MN3 a:OEX601 3.4 84.9 1.0
MN1 a:OEX601 3.5 84.0 1.0
OE1 a:GLU189 3.6 87.8 1.0
OXT a:ALA344 3.7 86.4 1.0
C a:ALA344 3.7 86.5 1.0
MN4 a:OEX601 3.8 87.7 1.0
NH1 c:ARG357 3.8 87.8 1.0
NH2 c:ARG357 3.8 85.3 1.0
O3 a:OEX601 3.9 84.7 1.0
O4 a:OEX601 4.0 88.0 1.0
OE2 a:GLU189 4.2 86.6 1.0
CD a:GLU189 4.3 86.0 1.0
CZ c:ARG357 4.3 88.9 1.0
CB a:ASP170 4.7 83.1 1.0
OE1 a:GLN165 4.7 85.3 1.0
OH a:TYR161 4.9 83.8 1.0
CB a:GLN165 5.0 83.7 1.0

Calcium binding site 6 out of 8 in 5e7c

Go back to Calcium Binding Sites List in 5e7c
Calcium binding site 6 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca603

b:0.7
occ:1.00
 OD1 b:ASN438 3.4 90.5 1.0
OE2 b:GLU435 4.1 95.1 0.5
OE1 o:GLU181 4.5 0.9 1.0
O b:SER439 4.5 84.0 1.0
CG b:ASN438 4.6 88.6 1.0
OE1 b:GLU435 4.8 93.8 0.5
CD b:GLU435 4.8 92.8 0.5

Calcium binding site 7 out of 8 in 5e7c

Go back to Calcium Binding Sites List in 5e7c
Calcium binding site 7 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca102

b:0.0
occ:1.00
 OXT f:ARG45 2.7 92.2 1.0
O f:ARG45 3.0 91.9 1.0
OE1 v:GLU23 3.1 0.1 1.0
C f:ARG45 3.3 92.5 1.0
OE2 v:GLU23 3.6 0.9 1.0
CD v:GLU23 3.7 0.4 1.0
CA f:ARG45 4.8 92.8 1.0
CG v:GLU23 5.0 0.6 1.0

Calcium binding site 8 out of 8 in 5e7c

Go back to Calcium Binding Sites List in 5e7c
Calcium binding site 8 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:0.7
occ:1.00
 O o:THR138 2.4 0.0 1.0
O o:VAL201 2.5 0.9 1.0
OD1 o:ASN200 2.6 0.3 1.0
C o:THR138 3.4 0.1 1.0
C o:VAL201 3.6 0.5 1.0
CG o:ASN200 3.7 0.1 1.0
N o:SER139 4.1 1.0 1.0
ND2 o:ASN200 4.1 0.1 1.0
CA o:SER139 4.1 1.0 1.0
N o:VAL201 4.2 99.8 1.0
CA o:THR138 4.3 0.1 1.0
O o:THR140 4.3 0.6 1.0
CA o:VAL201 4.4 0.0 1.0
C o:SER139 4.5 0.7 1.0
N o:ALA202 4.6 0.0 1.0
C o:ASN200 4.6 99.5 1.0
CA o:ALA202 4.7 0.6 1.0
CB o:THR138 4.8 0.0 1.0
N o:THR140 4.9 0.4 1.0
CB o:VAL201 4.9 0.2 1.0
O o:SER139 4.9 0.6 1.0
CB o:ASN200 4.9 100.0 1.0

Reference:

K.Ayyer, O.M.Yefanov, D.Oberthur, S.Roy-Chowdhury, L.Galli, V.Mariani, S.Basu, J.Coe, C.E.Conrad, R.Fromme, A.Schaffer, K.Dorner, D.James, C.Kupitz, M.Metz, G.Nelson, P.L.Xavier, K.R.Beyerlein, M.Schmidt, I.Sarrou, J.C.Spence, U.Weierstall, T.A.White, J.H.Yang, Y.Zhao, M.Liang, A.Aquila, M.S.Hunter, J.S.Robinson, J.E.Koglin, S.Boutet, P.Fromme, A.Barty, H.N.Chapman. Macromolecular Diffractive Imaging Using Imperfect Crystals. Nature V. 530 202 2016.
ISSN: ESSN 1476-4687
PubMed: 26863980
DOI: 10.1038/NATURE16949
Page generated: Sun Jul 14 18:23:55 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy