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Chlorine 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
Calcium (Ca) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data, PDB code: 5e7c:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5e7c

Go back to Chlorine Binding Sites List in 5e7c
Chlorine binding site 1 out of 6 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl602

b:65.5
occ:1.00
 ND2 A:ASN181 3.1 59.9 1.0
N A:GLU333 3.6 61.6 1.0
CB A:HIS332 3.6 61.1 1.0
NZ D:LYS317 3.6 64.9 1.0
CA A:HIS332 3.7 61.8 1.0
CG A:GLU333 3.8 62.3 1.0
CG2 A:VAL185 3.9 60.7 1.0
OD1 A:ASN181 3.9 62.9 1.0
CD1 D:LEU321 3.9 59.7 1.0
CG A:ASN181 3.9 60.6 1.0
CD2 D:LEU321 4.0 59.9 1.0
CE D:LYS317 4.1 61.8 1.0
C A:HIS332 4.1 61.7 1.0
CG D:LEU321 4.2 59.6 1.0
OE2 A:GLU333 4.4 62.8 1.0
CB D:LYS317 4.4 59.4 1.0
CD A:GLU333 4.5 62.5 1.0
CA A:GLU333 4.5 61.4 1.0
CG A:HIS332 4.6 61.1 1.0
CB A:GLU333 4.7 61.8 1.0
O D:LYS317 4.8 59.6 1.0
CD2 A:HIS332 4.8 60.6 1.0
CG D:LYS317 4.9 60.8 1.0

Chlorine binding site 2 out of 6 in 5e7c

Go back to Chlorine Binding Sites List in 5e7c
Chlorine binding site 2 out of 6 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:62.6
occ:1.00
 N C:GLU354 3.3 62.8 1.0
CD2 A:PHE339 3.4 62.4 1.0
N A:ASN338 3.5 62.4 1.0
CA C:GLY353 3.8 63.4 1.0
N A:PHE339 3.9 62.3 1.0
CB C:GLU354 4.0 63.1 1.0
C C:GLY353 4.0 63.3 1.0
CE2 A:PHE339 4.1 63.0 1.0
CA A:HIS337 4.1 62.1 1.0
CA C:GLU354 4.2 62.3 1.0
CG A:PHE339 4.2 63.0 1.0
N C:THR355 4.3 62.0 1.0
O A:ALA336 4.3 62.3 1.0
O C:GLY352 4.3 63.2 1.0
CB A:PHE339 4.3 62.7 1.0
C A:HIS337 4.3 62.1 1.0
CA A:ASN338 4.4 62.4 1.0
CG C:GLU354 4.5 62.3 1.0
CB A:ASN338 4.5 63.0 1.0
C A:ASN338 4.7 62.4 1.0
CA A:PHE339 4.7 62.6 1.0
CB A:HIS337 4.8 61.9 1.0
C C:GLU354 4.8 62.1 1.0
O A:PHE339 4.9 62.9 1.0
N C:GLY353 4.9 63.4 1.0
NE2 C:GLN313 5.0 62.0 1.0

Chlorine binding site 3 out of 6 in 5e7c

Go back to Chlorine Binding Sites List in 5e7c
Chlorine binding site 3 out of 6 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cl201

b:91.6
occ:1.00
 NZ U:LYS104 4.0 66.7 1.0
OD2 V:ASP53 4.1 67.4 1.0
NH1 V:ARG55 4.5 65.9 0.6

Chlorine binding site 4 out of 6 in 5e7c

Go back to Chlorine Binding Sites List in 5e7c
Chlorine binding site 4 out of 6 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl602

b:86.1
occ:1.00
 N a:GLU333 3.3 82.2 1.0
ND2 a:ASN181 3.4 80.5 1.0
CB a:HIS332 3.4 81.8 1.0
CA a:HIS332 3.5 82.4 1.0
NZ d:LYS317 3.5 85.6 1.0
CD2 d:LEU321 3.6 80.5 1.0
CG a:GLU333 3.8 83.0 1.0
C a:HIS332 3.9 82.3 1.0
CD1 d:LEU321 4.0 80.3 1.0
CG d:LEU321 4.1 80.2 1.0
CG2 a:VAL185 4.2 81.3 1.0
CE d:LYS317 4.3 82.5 1.0
OD1 a:ASN181 4.3 83.6 1.0
CG a:ASN181 4.3 81.2 1.0
CB d:LYS317 4.3 80.0 1.0
CA a:GLU333 4.4 82.0 1.0
OE2 a:GLU333 4.5 83.5 1.0
O d:LYS317 4.5 80.3 1.0
CG a:HIS332 4.5 81.8 1.0
CD a:GLU333 4.6 83.2 1.0
CB a:GLU333 4.7 82.4 1.0
CG d:LYS317 4.7 81.5 1.0
N a:HIS332 4.8 82.3 1.0
C d:LYS317 4.9 80.1 1.0
CD2 a:HIS332 4.9 81.3 1.0
CA d:LYS317 5.0 80.3 1.0

Chlorine binding site 5 out of 6 in 5e7c

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Cl501

b:83.2
occ:1.00
 N c:GLU354 3.2 83.4 1.0
N a:ASN338 3.3 83.0 1.0
CA c:GLY353 3.4 84.0 1.0
CD2 a:PHE339 3.6 83.1 1.0
C c:GLY353 3.8 84.0 1.0
CA a:HIS337 3.9 82.8 1.0
N a:PHE339 3.9 83.0 1.0
O a:ALA336 4.0 83.0 1.0
CB c:GLU354 4.0 83.8 1.0
C a:HIS337 4.1 82.7 1.0
CE2 a:PHE339 4.2 83.7 1.0
CA c:GLU354 4.2 82.9 1.0
CA a:ASN338 4.3 83.1 1.0
O c:GLY352 4.3 83.9 1.0
CB a:ASN338 4.4 83.6 1.0
CG c:GLU354 4.4 82.9 1.0
CG a:PHE339 4.4 83.7 1.0
N c:THR355 4.5 82.6 1.0
CB a:PHE339 4.5 83.3 1.0
N c:GLY353 4.6 84.0 1.0
CB a:HIS337 4.6 82.5 1.0
C a:ASN338 4.6 83.1 1.0
CA a:PHE339 4.8 83.2 1.0
C a:ALA336 4.8 83.1 1.0
N a:HIS337 4.9 82.4 1.0
C c:GLY352 4.9 84.2 1.0
O c:GLY353 4.9 84.5 1.0
CG a:ASN338 4.9 83.7 1.0
O a:PHE339 5.0 83.6 1.0
C c:GLU354 5.0 82.8 1.0

Chlorine binding site 6 out of 6 in 5e7c

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
u:Cl201

b:0.2
occ:1.00
 OD2 v:ASP53 3.9 88.1 1.0
NZ u:LYS104 4.0 87.4 1.0
CE u:LYS104 4.7 88.7 1.0
NH1 v:ARG55 4.8 86.5 0.6

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: Fri Jul 26 07:07:56 2024

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