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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

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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

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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

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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: Wed Jul 9 05:28:27 2025

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