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

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 5e7c

Go back to Iron Binding Sites List in 5e7c
Iron 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 Iron with other atoms in the Fe 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:Fe613

b:67.4
occ:1.00
NE2 D:HIS268 2.4 65.8 1.0
NE2 A:HIS272 2.4 67.1 1.0
NE2 A:HIS215 2.4 65.3 1.0
O2 A:BCT604 2.5 79.9 1.0
NE2 D:HIS214 2.5 63.2 1.0
O1 A:BCT604 2.5 80.7 1.0
C A:BCT604 3.0 81.2 1.0
CE1 A:HIS215 3.2 65.8 1.0
CE1 A:HIS272 3.2 67.4 1.0
CE1 D:HIS268 3.3 66.4 1.0
CE1 D:HIS214 3.4 63.9 1.0
CD2 D:HIS268 3.5 65.4 1.0
CD2 A:HIS272 3.5 68.0 1.0
CD2 D:HIS214 3.5 63.5 1.0
CD2 A:HIS215 3.5 63.3 1.0
O3 A:BCT604 4.1 82.8 1.0
ND1 A:HIS272 4.4 67.5 1.0
ND1 A:HIS215 4.4 65.8 1.0
ND1 D:HIS268 4.4 65.8 1.0
CG2 A:VAL219 4.5 67.7 1.0
CG A:HIS272 4.6 68.0 1.0
CG D:HIS268 4.6 64.5 1.0
ND1 D:HIS214 4.6 63.2 1.0
CG A:HIS215 4.6 65.8 1.0
CG D:HIS214 4.7 63.6 1.0
CG2 D:VAL218 4.9 64.8 1.0
OH D:TYR244 5.0 72.8 1.0

Iron binding site 2 out of 6 in 5e7c

Go back to Iron Binding Sites List in 5e7c
Iron 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 Iron with other atoms in the Fe binding site number 2 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe102

b:80.8
occ:1.00
FE E:HEM102 0.0 80.8 1.0
NB E:HEM102 2.0 81.6 1.0
NC E:HEM102 2.0 81.0 1.0
NA E:HEM102 2.1 82.7 1.0
ND E:HEM102 2.2 81.5 1.0
NE2 E:HIS23 2.4 85.9 1.0
NE2 F:HIS24 2.4 78.7 1.0
C4B E:HEM102 3.0 82.2 1.0
C1B E:HEM102 3.0 83.1 1.0
C1C E:HEM102 3.0 80.5 1.0
C1A E:HEM102 3.1 83.2 1.0
C4A E:HEM102 3.1 83.0 1.0
CD2 F:HIS24 3.1 78.2 1.0
C4C E:HEM102 3.1 80.7 1.0
C4D E:HEM102 3.1 82.8 1.0
C1D E:HEM102 3.1 81.6 1.0
CD2 E:HIS23 3.2 85.7 1.0
CE1 E:HIS23 3.3 86.0 1.0
CHC E:HEM102 3.4 80.7 1.0
CHB E:HEM102 3.4 83.2 1.0
CHA E:HEM102 3.4 82.6 1.0
CHD E:HEM102 3.5 80.8 1.0
CE1 F:HIS24 3.5 79.5 1.0
C2A E:HEM102 4.2 84.0 1.0
C3A E:HEM102 4.2 84.2 1.0
C3B E:HEM102 4.2 82.7 1.0
C2B E:HEM102 4.2 83.3 1.0
C2C E:HEM102 4.3 80.4 1.0
C3D E:HEM102 4.3 82.5 1.0
C3C E:HEM102 4.3 81.0 1.0
C2D E:HEM102 4.3 81.8 1.0
CG F:HIS24 4.3 78.4 1.0
ND1 E:HIS23 4.3 85.3 1.0
CG E:HIS23 4.3 86.6 1.0
ND1 F:HIS24 4.5 78.4 1.0
NE1 F:TRP20 4.7 80.9 1.0
CZ2 F:TRP20 4.8 82.7 1.0
OG1 E:THR26 4.9 82.9 1.0
CG2 E:ILE22 5.0 88.6 1.0
CE2 F:TRP20 5.0 80.9 1.0

Iron binding site 3 out of 6 in 5e7c

Go back to Iron Binding Sites List in 5e7c
Iron 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 Iron with other atoms in the Fe 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:Fe202

b:65.7
occ:1.00
FE V:HEM202 0.0 65.7 1.0
NA V:HEM202 2.0 64.8 1.0
NB V:HEM202 2.0 64.9 1.0
NC V:HEM202 2.1 64.6 1.0
ND V:HEM202 2.1 65.5 1.0
NE2 V:HIS41 2.3 64.4 1.0
NE2 V:HIS92 2.4 68.6 1.0
C1B V:HEM202 3.0 65.3 1.0
C4A V:HEM202 3.0 65.5 1.0
C4B V:HEM202 3.0 64.7 1.0
C1A V:HEM202 3.0 65.0 1.0
C4C V:HEM202 3.1 65.6 1.0
C4D V:HEM202 3.1 64.6 1.0
C1C V:HEM202 3.1 66.1 1.0
C1D V:HEM202 3.1 65.5 1.0
CD2 V:HIS41 3.1 63.6 1.0
CD2 V:HIS92 3.3 68.0 1.0
CE1 V:HIS41 3.3 62.9 1.0
CHB V:HEM202 3.4 65.3 1.0
CE1 V:HIS92 3.4 68.3 1.0
CHA V:HEM202 3.4 64.0 1.0
CHC V:HEM202 3.4 65.6 1.0
CHD V:HEM202 3.5 65.1 1.0
C2B V:HEM202 4.1 65.6 1.0
C3B V:HEM202 4.2 66.2 1.0
C3A V:HEM202 4.2 65.3 1.0
C2A V:HEM202 4.2 65.4 1.0
CG V:HIS41 4.3 63.4 1.0
C3C V:HEM202 4.3 65.3 1.0
C2C V:HEM202 4.3 65.0 1.0
C3D V:HEM202 4.3 65.3 1.0
C2D V:HEM202 4.3 64.8 1.0
ND1 V:HIS41 4.3 63.3 1.0
CG V:HIS92 4.4 68.6 1.0
ND1 V:HIS92 4.5 68.8 1.0
CE1 V:TYR75 4.7 68.4 1.0

Iron binding site 4 out of 6 in 5e7c

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Iron 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 Iron with other atoms in the Fe 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:Fe615

b:88.0
occ:1.00
NE2 d:HIS268 2.4 86.5 1.0
NE2 a:HIS272 2.4 87.8 1.0
NE2 a:HIS215 2.5 85.9 1.0
NE2 d:HIS214 2.5 83.9 1.0
O2 a:BCT603 2.5 0.5 1.0
O1 a:BCT603 2.6 0.3 1.0
C a:BCT603 3.0 0.9 1.0
CE1 a:HIS272 3.2 88.1 1.0
CE1 a:HIS215 3.3 86.4 1.0
CE1 d:HIS268 3.4 87.1 1.0
CD2 d:HIS268 3.4 86.0 1.0
CD2 d:HIS214 3.4 84.1 1.0
CE1 d:HIS214 3.5 84.5 1.0
CD2 a:HIS272 3.5 88.7 1.0
CD2 a:HIS215 3.5 84.0 1.0
O3 a:BCT603 4.3 0.4 1.0
ND1 a:HIS272 4.4 88.2 1.0
ND1 d:HIS268 4.5 86.5 1.0
ND1 a:HIS215 4.5 86.4 1.0
CG d:HIS268 4.5 85.2 1.0
CG d:HIS214 4.6 84.3 1.0
CG a:HIS272 4.6 88.7 1.0
ND1 d:HIS214 4.6 83.8 1.0
CG a:HIS215 4.6 86.5 1.0
CG2 a:VAL219 4.7 88.4 1.0
CG2 d:VAL218 4.8 85.5 1.0

Iron binding site 5 out of 6 in 5e7c

Go back to Iron Binding Sites List in 5e7c
Iron 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 Iron with other atoms in the Fe binding site number 5 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe102

b:0.5
occ:1.00
FE e:HEM102 0.0 0.5 1.0
NC e:HEM102 2.0 0.7 1.0
NB e:HEM102 2.1 0.2 1.0
NA e:HEM102 2.1 0.3 1.0
ND e:HEM102 2.1 0.1 1.0
NE2 f:HIS24 2.4 99.3 1.0
NE2 e:HIS23 2.4 0.6 1.0
C1A e:HEM102 3.0 0.8 1.0
C1C e:HEM102 3.0 0.2 1.0
C4D e:HEM102 3.0 0.4 1.0
C4C e:HEM102 3.1 0.4 1.0
C4B e:HEM102 3.1 0.8 1.0
C4A e:HEM102 3.1 0.7 1.0
C1D e:HEM102 3.1 0.2 1.0
C1B e:HEM102 3.1 0.8 1.0
CE1 e:HIS23 3.3 0.6 1.0
CD2 f:HIS24 3.3 98.8 1.0
CE1 f:HIS24 3.3 0.1 1.0
CHA e:HEM102 3.4 0.2 1.0
CD2 e:HIS23 3.4 0.3 1.0
CHC e:HEM102 3.4 0.4 1.0
CHD e:HEM102 3.4 0.4 1.0
CHB e:HEM102 3.5 0.8 1.0
C2A e:HEM102 4.2 0.7 1.0
C3A e:HEM102 4.2 0.8 1.0
C3D e:HEM102 4.2 0.2 1.0
C2C e:HEM102 4.3 0.0 1.0
C2D e:HEM102 4.3 0.5 1.0
C3C e:HEM102 4.3 0.6 1.0
C3B e:HEM102 4.3 0.3 1.0
C2B e:HEM102 4.3 0.9 1.0
ND1 e:HIS23 4.4 1.0 1.0
ND1 f:HIS24 4.4 99.0 1.0
CG f:HIS24 4.5 99.0 1.0
CG e:HIS23 4.5 0.2 1.0
CZ2 f:TRP20 4.8 0.3 1.0
NE1 f:TRP20 4.8 0.5 1.0

Iron binding site 6 out of 6 in 5e7c

Go back to Iron Binding Sites List in 5e7c
Iron 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 Iron with other atoms in the Fe binding site number 6 of Macromolecular Diffractive Imaging Using Imperfect Crystals - Bragg Data within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:86.4
occ:1.00
FE v:HEM201 0.0 86.4 1.0
NA v:HEM201 2.0 85.5 1.0
NB v:HEM201 2.1 85.5 1.0
NC v:HEM201 2.1 85.2 1.0
ND v:HEM201 2.1 86.1 1.0
NE2 v:HIS41 2.3 85.0 1.0
NE2 v:HIS92 2.4 89.3 1.0
C1B v:HEM201 3.0 85.9 1.0
C1A v:HEM201 3.0 85.6 1.0
C4B v:HEM201 3.0 85.3 1.0
C4A v:HEM201 3.0 86.1 1.0
C4D v:HEM201 3.1 85.3 1.0
C1C v:HEM201 3.1 86.8 1.0
C1D v:HEM201 3.1 86.2 1.0
C4C v:HEM201 3.1 86.2 1.0
CD2 v:HIS92 3.3 88.7 1.0
CD2 v:HIS41 3.3 84.3 1.0
CE1 v:HIS41 3.3 83.5 1.0
CHA v:HEM201 3.4 84.6 1.0
CHB v:HEM201 3.4 85.9 1.0
CE1 v:HIS92 3.4 89.0 1.0
CHC v:HEM201 3.4 86.3 1.0
CHD v:HEM201 3.5 85.7 1.0
C2B v:HEM201 4.2 86.3 1.0
C3B v:HEM201 4.2 86.9 1.0
C2A v:HEM201 4.2 86.0 1.0
C3A v:HEM201 4.3 86.0 1.0
C3D v:HEM201 4.3 85.9 1.0
C2D v:HEM201 4.3 85.4 1.0
C2C v:HEM201 4.3 85.7 1.0
C3C v:HEM201 4.3 86.0 1.0
ND1 v:HIS41 4.4 83.9 1.0
CG v:HIS41 4.4 84.0 1.0
CG v:HIS92 4.5 89.2 1.0
ND1 v:HIS92 4.5 89.5 1.0
CE1 v:TYR75 4.7 89.1 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: Tue Aug 5 20:53:27 2025

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