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Manganese 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
Iron (Fe) 6 atoms
Calcium (Ca) 8 atoms
Chlorine (Cl) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese where determined in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data, PDB code: 5e7c:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5e7c

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Manganese binding site 1 out of 8 in the Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn601

b:63.4
occ:1.00
 MN1 A:OEX601 0.0 63.4 1.0
O3 A:OEX601 1.8 64.0 1.0
O1 A:OEX601 1.9 63.2 1.0
OE2 A:GLU189 2.2 65.9 1.0
OD2 A:ASP342 2.4 64.2 1.0
NE2 A:HIS332 2.4 60.8 1.0
O5 A:OEX601 2.6 64.9 1.0
MN2 A:OEX601 2.8 63.6 1.0
CD A:GLU189 3.2 65.3 1.0
CD2 A:HIS332 3.2 60.6 1.0
CG A:ASP342 3.3 63.1 1.0
MN3 A:OEX601 3.3 64.2 1.0
CE1 A:HIS332 3.4 63.6 1.0
CA1 A:OEX601 3.5 65.3 1.0
OD1 A:ASP342 3.5 61.5 1.0
O2 A:OEX601 3.7 66.0 1.0
OE1 A:GLU333 3.8 65.0 1.0
OE1 A:GLU189 3.9 67.1 1.0
NE2 A:HIS337 4.1 63.5 1.0
CG A:GLU189 4.1 64.7 1.0
CG A:HIS332 4.4 61.1 1.0
ND1 A:HIS332 4.4 59.9 1.0
OE1 C:GLU354 4.5 63.3 1.0
CB A:ASP342 4.6 62.8 1.0
CG1 A:VAL185 4.7 61.0 1.0
CD A:GLU333 4.7 62.5 1.0
OXT A:ALA344 4.7 65.8 1.0
OE2 C:GLU354 4.7 63.9 1.0
CE1 A:HIS337 4.8 61.4 1.0
OE2 A:GLU333 4.9 62.8 1.0
MN4 A:OEX601 5.0 67.0 1.0

Manganese binding site 2 out of 8 in 5e7c

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Manganese 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 Manganese with other atoms in the Mn 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:Mn601

b:63.6
occ:1.00
 MN2 A:OEX601 0.0 63.6 1.0
O1 A:OEX601 2.1 63.2 1.0
O3 A:OEX601 2.1 64.0 1.0
O2 A:OEX601 2.1 66.0 1.0
OD1 A:ASP342 2.3 61.5 1.0
OXT A:ALA344 2.3 65.8 1.0
OE1 C:GLU354 2.4 63.3 1.0
MN1 A:OEX601 2.8 63.4 1.0
MN3 A:OEX601 2.9 64.2 1.0
CG A:ASP342 3.1 63.1 1.0
CD C:GLU354 3.3 63.5 1.0
OD2 A:ASP342 3.3 64.2 1.0
C A:ALA344 3.3 65.8 1.0
CA1 A:OEX601 3.4 65.3 1.0
OE2 C:GLU354 3.5 63.9 1.0
O A:ALA344 3.6 66.4 1.0
O5 A:OEX601 3.8 64.9 1.0
NE2 A:HIS337 4.2 63.5 1.0
NH2 C:ARG357 4.3 64.7 1.0
NH1 C:ARG357 4.5 67.2 1.0
O4 A:OEX601 4.5 67.4 1.0
CB A:ASP342 4.5 62.8 1.0
CG C:GLU354 4.6 62.3 1.0
CA A:ALA344 4.6 65.5 1.0
CD2 A:HIS337 4.6 61.3 1.0
N A:ALA344 4.6 65.5 1.0
CZ C:ARG357 4.7 68.2 1.0
OE1 A:GLU333 4.7 65.0 1.0
NE2 A:HIS332 4.7 60.8 1.0
OE2 A:GLU189 4.8 65.9 1.0
CB C:GLU354 4.8 63.1 1.0
CA A:ASP342 4.9 63.3 1.0

Manganese binding site 3 out of 8 in 5e7c

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Manganese 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 Manganese with other atoms in the Mn binding site number 3 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:64.2
occ:1.00
 MN3 A:OEX601 0.0 64.2 1.0
O2 A:OEX601 1.9 66.0 1.0
O4 A:OEX601 2.1 67.4 1.0
O3 A:OEX601 2.1 64.0 1.0
OE1 A:GLU333 2.3 65.0 1.0
O5 A:OEX601 2.4 64.9 1.0
OE2 C:GLU354 2.4 63.9 1.0
MN2 A:OEX601 2.9 63.6 1.0
MN4 A:OEX601 3.0 67.0 1.0
CD A:GLU333 3.2 62.5 1.0
CD C:GLU354 3.2 63.5 1.0
MN1 A:OEX601 3.3 63.4 1.0
CA1 A:OEX601 3.4 65.3 1.0
OE1 C:GLU354 3.4 63.3 1.0
OE2 A:GLU333 3.5 62.8 1.0
O1 A:OEX601 3.5 63.2 1.0
NH2 C:ARG357 3.6 64.7 1.0
OD2 A:ASP170 4.3 63.9 1.0
NE2 A:HIS332 4.4 60.8 1.0
NE2 A:HIS337 4.5 63.5 1.0
CG A:GLU333 4.6 62.3 1.0
CG C:GLU354 4.6 62.3 1.0
CD2 A:HIS332 4.6 60.6 1.0
CZ C:ARG357 4.7 68.2 1.0
OXT A:ALA344 4.8 65.8 1.0
CB A:GLU333 4.9 61.8 1.0
NH1 C:ARG357 5.0 67.2 1.0
OE2 A:GLU189 5.0 65.9 1.0
OD1 A:ASP342 5.0 61.5 1.0

Manganese binding site 4 out of 8 in 5e7c

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Manganese 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 Manganese with other atoms in the Mn 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:Mn601

b:67.0
occ:1.00
 MN4 A:OEX601 0.0 67.0 1.0
O4 A:OEX601 2.1 67.4 1.0
OE2 A:GLU333 2.4 62.8 1.0
OD2 A:ASP170 2.5 63.9 1.0
O5 A:OEX601 2.5 64.9 1.0
MN3 A:OEX601 3.0 64.2 1.0
CD A:GLU333 3.3 62.5 1.0
OE1 A:GLU333 3.5 65.0 1.0
CG A:ASP170 3.7 63.3 1.0
O2 A:OEX601 3.8 66.0 1.0
CA1 A:OEX601 3.8 65.3 1.0
OD1 A:ASP61 4.1 64.0 1.0
O A:SER169 4.2 61.3 1.0
OD1 A:ASP170 4.4 64.6 1.0
NH2 C:ARG357 4.4 64.7 1.0
CG A:GLU333 4.6 62.3 1.0
CA A:ASP170 4.6 62.3 1.0
O3 A:OEX601 4.7 64.0 1.0
CB A:ASP170 4.7 62.4 1.0
C A:SER169 4.8 61.0 1.0
OG A:SER169 4.9 59.9 1.0
N A:ASP170 5.0 61.7 1.0
MN1 A:OEX601 5.0 63.4 1.0
CG A:ASP61 5.0 63.4 1.0

Manganese binding site 5 out of 8 in 5e7c

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Manganese 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 Manganese with other atoms in the Mn 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:Mn601

b:84.0
occ:1.00
 MN1 a:OEX601 0.0 84.0 1.0
O3 a:OEX601 1.8 84.7 1.0
O1 a:OEX601 1.9 83.9 1.0
OE2 a:GLU189 2.2 86.6 1.0
OD2 a:ASP342 2.3 84.9 1.0
NE2 a:HIS332 2.4 81.4 1.0
O5 a:OEX601 2.6 85.5 1.0
MN2 a:OEX601 2.8 84.3 1.0
CD a:GLU189 3.2 86.0 1.0
CG a:ASP342 3.2 83.8 1.0
MN3 a:OEX601 3.3 84.9 1.0
CD2 a:HIS332 3.3 81.3 1.0
OD1 a:ASP342 3.4 82.1 1.0
CE1 a:HIS332 3.5 84.2 1.0
CA1 a:OEX601 3.5 86.0 1.0
OE1 a:GLU189 3.7 87.8 1.0
O2 a:OEX601 3.7 86.6 1.0
OE1 a:GLU333 3.9 85.6 1.0
NE2 a:HIS337 4.1 84.1 1.0
OE1 c:GLU354 4.3 84.0 1.0
CG a:GLU189 4.3 85.4 1.0
CG a:HIS332 4.5 81.8 1.0
ND1 a:HIS332 4.5 80.6 1.0
OE2 c:GLU354 4.6 84.6 1.0
CB a:ASP342 4.6 83.4 1.0
OXT a:ALA344 4.6 86.4 1.0
CG1 a:VAL185 4.6 81.7 1.0
CD a:GLU333 4.7 83.2 1.0
CE1 a:HIS337 4.8 82.0 1.0
CD c:GLU354 4.9 84.2 1.0
MN4 a:OEX601 5.0 87.7 1.0

Manganese binding site 6 out of 8 in 5e7c

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Manganese 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 Manganese with other atoms in the Mn binding site number 6 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:84.3
occ:1.00
 MN2 a:OEX601 0.0 84.3 1.0
O1 a:OEX601 2.1 83.9 1.0
O3 a:OEX601 2.1 84.7 1.0
O2 a:OEX601 2.1 86.6 1.0
OE1 c:GLU354 2.3 84.0 1.0
OXT a:ALA344 2.3 86.4 1.0
OD1 a:ASP342 2.4 82.1 1.0
MN1 a:OEX601 2.8 84.0 1.0
MN3 a:OEX601 2.9 84.9 1.0
CD c:GLU354 3.1 84.2 1.0
CG a:ASP342 3.2 83.8 1.0
CA1 a:OEX601 3.4 86.0 1.0
C a:ALA344 3.4 86.5 1.0
OD2 a:ASP342 3.4 84.9 1.0
OE2 c:GLU354 3.4 84.6 1.0
O a:ALA344 3.8 87.1 1.0
O5 a:OEX601 3.8 85.5 1.0
NH2 c:ARG357 4.1 85.3 1.0
NE2 a:HIS337 4.2 84.1 1.0
CG c:GLU354 4.4 82.9 1.0
O4 a:OEX601 4.5 88.0 1.0
CB c:GLU354 4.5 83.8 1.0
NH1 c:ARG357 4.6 87.8 1.0
CZ c:ARG357 4.6 88.9 1.0
CD2 a:HIS337 4.6 81.9 1.0
N a:ALA344 4.6 86.1 1.0
CB a:ASP342 4.6 83.4 1.0
CA a:ALA344 4.6 86.1 1.0
OE1 a:GLU333 4.7 85.6 1.0
OE2 a:GLU189 4.8 86.6 1.0
NE2 a:HIS332 4.9 81.4 1.0

Manganese binding site 7 out of 8 in 5e7c

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Manganese 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 Manganese with other atoms in the Mn binding site number 7 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:84.9
occ:1.00
 MN3 a:OEX601 0.0 84.9 1.0
O2 a:OEX601 1.9 86.6 1.0
O4 a:OEX601 2.1 88.0 1.0
O3 a:OEX601 2.1 84.7 1.0
OE1 a:GLU333 2.3 85.6 1.0
OE2 c:GLU354 2.4 84.6 1.0
O5 a:OEX601 2.4 85.5 1.0
MN2 a:OEX601 2.9 84.3 1.0
MN4 a:OEX601 3.0 87.7 1.0
CD c:GLU354 3.2 84.2 1.0
MN1 a:OEX601 3.3 84.0 1.0
CD a:GLU333 3.3 83.2 1.0
CA1 a:OEX601 3.4 86.0 1.0
OE1 c:GLU354 3.4 84.0 1.0
NH2 c:ARG357 3.5 85.3 1.0
O1 a:OEX601 3.5 83.9 1.0
OE2 a:GLU333 3.7 83.5 1.0
OD2 a:ASP170 4.3 84.5 1.0
CG c:GLU354 4.4 82.9 1.0
NE2 a:HIS337 4.5 84.1 1.0
NE2 a:HIS332 4.6 81.4 1.0
CG a:GLU333 4.6 83.0 1.0
CZ c:ARG357 4.6 88.9 1.0
CD2 a:HIS332 4.8 81.3 1.0
OXT a:ALA344 4.8 86.4 1.0
CB a:GLU333 4.8 82.4 1.0
OD1 a:ASP342 5.0 82.1 1.0

Manganese binding site 8 out of 8 in 5e7c

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Manganese 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 Manganese with other atoms in the Mn binding site number 8 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:87.7
occ:1.00
 MN4 a:OEX601 0.0 87.7 1.0
O4 a:OEX601 2.1 88.0 1.0
OD2 a:ASP170 2.5 84.5 1.0
O5 a:OEX601 2.5 85.5 1.0
OE2 a:GLU333 2.5 83.5 1.0
MN3 a:OEX601 3.0 84.9 1.0
CD a:GLU333 3.2 83.2 1.0
OE1 a:GLU333 3.3 85.6 1.0
CG a:ASP170 3.7 84.0 1.0
O2 a:OEX601 3.8 86.6 1.0
CA1 a:OEX601 3.8 86.0 1.0
OD1 a:ASP61 3.9 84.7 1.0
O a:SER169 4.2 82.0 1.0
NH2 c:ARG357 4.4 85.3 1.0
OD1 a:ASP170 4.5 85.3 1.0
CA a:ASP170 4.5 82.9 1.0
CG a:GLU333 4.6 83.0 1.0
O3 a:OEX601 4.7 84.7 1.0
CB a:ASP170 4.7 83.1 1.0
C a:SER169 4.8 81.7 1.0
OG a:SER169 4.9 80.6 1.0
N a:ASP170 4.9 82.3 1.0
CG a:ASP61 4.9 84.1 1.0
MN1 a:OEX601 5.0 84.0 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: Sat Oct 5 23:59:52 2024

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