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Iron in PDB 3pcq: Femtosecond X-Ray Protein Nanocrystallography

Protein crystallography data

The structure of Femtosecond X-Ray Protein Nanocrystallography, PDB code: 3pcq was solved by H.N.Chapman, P.Fromme, A.Barty, T.A.White, R.A.Kirian, A.Aquila, M.S.Hunter, J.Schulz, D.P.Deponte, U.Weierstall, R.B.Doak, F.R.N.C.Maia, A.V.Martin, I.Schlichting, L.Lomb, N.Coppola, R.L.Shoeman, S.W.Epp, R.Hartmann, D.Rolles, A.Rudenko, L.Foucar, N.Kimmel, G.Weidenspointner, P.Holl, M.Liang, M.Barthelmess, C.Caleman, S.Boutet, M.J.Bogan, J.Krzywinski, C.Bostedt, S.Bajt, L.Gumprecht, B.Rudek, B.Erk, C.Schmidt, A.Homke, C.Reich, D.Pietschner, L.Struder, G.Hauser, H.Gorke, J.Ullrich, S.Herrmann, G.Schaller, F.Schopper, H.Soltau, K.-U.Kuhnel, M.Messerschmidt, J.D.Bozek, S.P.Hau-Riege, M.Frank, C.Y.Hampton, R.Sierra, D.Starodub, G.J.Williams, J.Hajdu, N.Timneanu, M.M.Seibert, J.Andreasson, A.Rocker, O.Jonsson, M.Svenda, S.Stern, K.Nass, R.Andritschke, C.-D.Schroter, F.Krasniqi, M.Bott, K.E.Schmidt, X.Wang, I.Grotjohann, J.M.Holton, T.R.M.Barends, R.Neutze, S.Marchesini, R.Fromme, S.Schorb, D.Rupp, M.Adolph, T.Gorkhover, I.Andersson, H.Hirsemann, G.Potdevin, H.Graafsma, B.Nilsson, J.C.H.Spence, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.12 / 8.98
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 281.000, 281.000, 165.200, 90.00, 90.00, 120.00
R / Rfree (%) 25.2 / 23.2

Other elements in 3pcq:

The structure of Femtosecond X-Ray Protein Nanocrystallography also contains other interesting chemical elements:

Magnesium (Mg) 96 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Femtosecond X-Ray Protein Nanocrystallography (pdb code 3pcq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Femtosecond X-Ray Protein Nanocrystallography, PDB code: 3pcq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 3pcq

Go back to Iron Binding Sites List in 3pcq
Iron binding site 1 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe848

b:26.9
occ:1.00
FE1 A:SF4848 0.0 26.9 1.0
S4 A:SF4848 2.3 25.9 1.0
S2 A:SF4848 2.3 25.9 1.0
S3 A:SF4848 2.3 25.8 1.0
SG B:CYS574 2.4 30.4 1.0
FE2 A:SF4848 2.7 27.5 1.0
FE4 A:SF4848 2.7 26.5 1.0
FE3 A:SF4848 2.7 27.0 1.0
CB B:CYS574 3.3 28.4 1.0
S1 A:SF4848 3.9 27.4 1.0
CA B:CYS574 3.9 29.7 1.0
CD1 A:ILE724 4.1 27.6 1.0
N B:CYS574 4.1 29.5 1.0
CZ3 B:TRP673 4.1 29.1 1.0
SG B:CYS565 4.6 27.2 1.0
CG2 A:ILE724 4.6 29.2 1.0
CE3 B:TRP673 4.7 29.2 1.0
SG A:CYS578 4.7 23.4 1.0
CB B:CYS565 4.8 29.6 1.0
CG1 A:ILE724 4.9 30.1 1.0
SG A:CYS587 5.0 27.4 1.0

Iron binding site 2 out of 12 in 3pcq

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Iron binding site 2 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe848

b:27.5
occ:1.00
FE2 A:SF4848 0.0 27.5 1.0
S1 A:SF4848 2.3 27.4 1.0
S3 A:SF4848 2.3 25.8 1.0
S4 A:SF4848 2.3 25.9 1.0
SG A:CYS587 2.4 27.4 1.0
FE1 A:SF4848 2.7 26.9 1.0
FE4 A:SF4848 2.7 26.5 1.0
FE3 A:SF4848 2.7 27.0 1.0
CB A:CYS587 3.3 21.9 1.0
S2 A:SF4848 3.9 25.9 1.0
CA A:CYS587 3.9 24.0 1.0
CD1 B:ILE708 3.9 23.3 1.0
CE3 B:TRP673 4.2 29.2 1.0
N A:CYS587 4.2 23.7 1.0
CZ3 B:TRP673 4.5 29.1 1.0
SG A:CYS578 4.5 23.4 1.0
CB A:CYS578 4.5 28.9 1.0
SG B:CYS565 4.7 27.2 1.0
CG1 B:ILE708 4.8 25.5 1.0
SG B:CYS574 4.9 30.4 1.0

Iron binding site 3 out of 12 in 3pcq

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Iron binding site 3 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe848

b:27.0
occ:1.00
FE3 A:SF4848 0.0 27.0 1.0
SG A:CYS578 2.2 23.4 1.0
S2 A:SF4848 2.2 25.9 1.0
S1 A:SF4848 2.3 27.4 1.0
S4 A:SF4848 2.3 25.9 1.0
FE4 A:SF4848 2.7 26.5 1.0
FE1 A:SF4848 2.7 26.9 1.0
FE2 A:SF4848 2.7 27.5 1.0
CB A:CYS578 3.3 28.9 1.0
S3 A:SF4848 3.9 25.8 1.0
CD B:PRO568 4.3 25.0 1.0
N A:GLY580 4.4 25.7 1.0
CA A:GLY580 4.5 23.5 1.0
N B:PRO568 4.5 26.5 1.0
CD1 A:ILE724 4.6 27.6 1.0
CA A:CYS578 4.7 29.7 1.0
C B:GLY567 4.7 27.1 1.0
O A:PRO577 4.7 32.6 1.0
CB B:PRO568 4.8 27.2 1.0
C A:GLY580 4.8 24.6 1.0
SG B:CYS565 4.8 27.2 1.0
SG A:CYS587 4.8 27.4 1.0
CA B:GLY567 4.9 27.2 1.0
SG B:CYS574 4.9 30.4 1.0
CA B:PRO568 5.0 28.3 1.0
C A:PRO577 5.0 31.9 1.0
CG B:PRO568 5.0 25.4 1.0
CA A:CYS587 5.0 24.0 1.0

Iron binding site 4 out of 12 in 3pcq

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Iron binding site 4 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe848

b:26.5
occ:1.00
FE4 A:SF4848 0.0 26.5 1.0
SG B:CYS565 2.3 27.2 1.0
S1 A:SF4848 2.3 27.4 1.0
S2 A:SF4848 2.3 25.9 1.0
S3 A:SF4848 2.3 25.8 1.0
FE3 A:SF4848 2.7 27.0 1.0
FE2 A:SF4848 2.7 27.5 1.0
FE1 A:SF4848 2.7 26.9 1.0
CB B:CYS565 3.3 29.6 1.0
S4 A:SF4848 3.9 25.9 1.0
N B:GLY567 4.3 30.2 1.0
CA B:GLY567 4.4 27.2 1.0
CD1 B:ILE708 4.4 23.3 1.0
CD A:PRO581 4.4 22.5 1.0
N A:PRO581 4.5 23.8 1.0
CA B:CYS565 4.7 31.7 1.0
CB A:PRO581 4.8 23.1 1.0
SG A:CYS578 4.8 23.4 1.0
C B:GLY567 4.8 27.1 1.0
SG B:CYS574 4.8 30.4 1.0
C A:GLY580 4.9 24.6 1.0
CA A:PRO581 4.9 23.9 1.0
O B:PRO564 4.9 32.9 1.0
SG A:CYS587 4.9 27.4 1.0
CA B:CYS574 5.0 29.7 1.0

Iron binding site 5 out of 12 in 3pcq

Go back to Iron Binding Sites List in 3pcq
Iron binding site 5 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:25.8
occ:1.00
FE1 C:SF4101 0.0 25.8 1.0
S2 C:SF4101 2.2 26.4 1.0
S3 C:SF4101 2.3 25.6 1.0
S4 C:SF4101 2.3 25.3 1.0
SG C:CYS50 2.4 28.6 1.0
FE4 C:SF4101 2.7 26.0 1.0
FE3 C:SF4101 2.7 26.1 1.0
FE2 C:SF4101 2.8 26.8 1.0
N C:CYS50 3.4 24.2 1.0
N C:LYS51 3.5 29.3 1.0
CB C:CYS50 3.7 26.1 1.0
S1 C:SF4101 3.9 24.6 1.0
CA C:CYS50 3.9 25.3 1.0
CD C:PRO21 4.1 34.5 1.0
N C:GLY49 4.1 25.9 1.0
C C:CYS50 4.2 28.3 1.0
C C:GLY49 4.2 25.1 1.0
N C:ARG52 4.2 29.3 1.0
CA C:LYS51 4.4 29.0 1.0
CA C:GLY49 4.4 23.3 1.0
CG2 C:VAL48 4.5 26.7 1.0
CG C:PRO21 4.7 34.2 1.0
SG C:CYS47 4.7 23.4 1.0
SG C:CYS53 4.7 33.7 1.0
C C:LYS51 4.8 29.1 1.0
SG C:CYS20 4.8 36.2 1.0
N C:VAL48 4.9 25.6 1.0
N C:CYS53 4.9 30.6 1.0

Iron binding site 6 out of 12 in 3pcq

Go back to Iron Binding Sites List in 3pcq
Iron binding site 6 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:26.8
occ:1.00
FE2 C:SF4101 0.0 26.8 1.0
S1 C:SF4101 2.2 24.6 1.0
S4 C:SF4101 2.3 25.3 1.0
S3 C:SF4101 2.3 25.6 1.0
SG C:CYS20 2.4 36.2 1.0
FE3 C:SF4101 2.7 26.1 1.0
FE4 C:SF4101 2.7 26.0 1.0
FE1 C:SF4101 2.8 25.8 1.0
CB C:CYS20 3.2 33.1 1.0
CA C:CYS20 3.8 35.3 1.0
S2 C:SF4101 3.9 26.4 1.0
CD C:PRO21 4.0 34.5 1.0
CG2 C:VAL24 4.1 30.8 1.0
CB C:VAL24 4.1 29.9 1.0
OG1 C:THR22 4.3 30.4 1.0
C C:CYS20 4.6 36.3 1.0
N C:PRO21 4.6 36.0 1.0
SG C:CYS50 4.7 28.6 1.0
CD1 C:LEU25 4.8 30.6 1.0
SG C:CYS47 4.9 23.4 1.0
CB C:CYS53 4.9 28.2 1.0
SG C:CYS53 4.9 33.7 1.0
CG C:LEU25 4.9 30.3 1.0
N C:CYS20 4.9 34.9 1.0
CG1 C:VAL24 4.9 27.2 1.0
N C:VAL24 5.0 32.6 1.0

Iron binding site 7 out of 12 in 3pcq

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Iron binding site 7 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:26.1
occ:1.00
FE3 C:SF4101 0.0 26.1 1.0
S4 C:SF4101 2.2 25.3 1.0
S1 C:SF4101 2.3 24.6 1.0
S2 C:SF4101 2.4 26.4 1.0
SG C:CYS53 2.4 33.7 1.0
FE2 C:SF4101 2.7 26.8 1.0
FE1 C:SF4101 2.7 25.8 1.0
FE4 C:SF4101 2.8 26.0 1.0
CB C:CYS53 3.1 28.2 1.0
S3 C:SF4101 3.9 25.6 1.0
N C:CYS53 4.0 30.6 1.0
CA C:CYS53 4.2 31.5 1.0
CG2 C:VAL66 4.2 31.0 1.0
N C:LYS51 4.5 29.3 1.0
CA C:LYS51 4.6 29.0 1.0
SG C:CYS50 4.7 28.6 1.0
N C:ARG52 4.7 29.3 1.0
CD1 C:LEU25 4.7 30.6 1.0
SG C:CYS47 4.8 23.4 1.0
C C:LYS51 4.9 29.1 1.0
SG C:CYS20 4.9 36.2 1.0

Iron binding site 8 out of 12 in 3pcq

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Iron binding site 8 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:26.0
occ:1.00
FE4 C:SF4101 0.0 26.0 1.0
S3 C:SF4101 2.2 25.6 1.0
S2 C:SF4101 2.3 26.4 1.0
SG C:CYS47 2.3 23.4 1.0
S1 C:SF4101 2.3 24.6 1.0
FE1 C:SF4101 2.7 25.8 1.0
FE2 C:SF4101 2.7 26.8 1.0
FE3 C:SF4101 2.8 26.1 1.0
CB C:CYS47 3.5 25.7 1.0
N C:GLY49 3.8 25.9 1.0
CA C:CYS47 3.8 25.7 1.0
S4 C:SF4101 3.9 25.3 1.0
N C:VAL48 4.0 25.6 1.0
C C:CYS47 4.2 25.9 1.0
CG2 C:VAL24 4.3 30.8 1.0
CA C:GLY49 4.3 23.3 1.0
CG2 C:VAL4 4.6 29.3 1.0
CB C:VAL24 4.7 29.9 1.0
N C:CYS50 4.8 24.2 1.0
SG C:CYS20 4.8 36.2 1.0
C C:VAL48 4.9 28.1 1.0
CG1 C:VAL24 4.9 27.2 1.0
C C:GLY49 5.0 25.1 1.0
SG C:CYS53 5.0 33.7 1.0

Iron binding site 9 out of 12 in 3pcq

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Iron binding site 9 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:35.7
occ:1.00
FE1 C:SF4102 0.0 35.7 1.0
S4 C:SF4102 2.3 33.1 1.0
S2 C:SF4102 2.3 34.1 1.0
S3 C:SF4102 2.3 34.2 1.0
SG C:CYS57 2.4 39.7 1.0
FE2 C:SF4102 2.7 34.5 1.0
FE4 C:SF4102 2.7 35.0 1.0
FE3 C:SF4102 2.7 35.5 1.0
CB C:CYS57 3.3 36.6 1.0
CA C:CYS57 3.8 37.8 1.0
S1 C:SF4102 3.9 34.5 1.0
CD C:PRO58 3.9 41.6 1.0
CB C:SER63 4.0 35.7 1.0
CG2 C:ILE64 4.5 29.3 1.0
C C:CYS57 4.6 39.9 1.0
SG C:CYS13 4.6 35.8 1.0
N C:PRO58 4.6 41.2 1.0
N C:ILE64 4.7 34.1 1.0
OG C:SER63 4.7 32.9 1.0
CG2 C:THR59 4.7 39.8 1.0
N C:SER63 4.8 32.7 1.0
N C:CYS57 4.8 35.4 1.0
SG C:CYS16 4.9 40.9 1.0
CA C:SER63 4.9 35.1 1.0
CB C:ILE64 4.9 32.1 1.0
SG C:CYS10 4.9 35.5 1.0

Iron binding site 10 out of 12 in 3pcq

Go back to Iron Binding Sites List in 3pcq
Iron binding site 10 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:34.5
occ:1.00
FE2 C:SF4102 0.0 34.5 1.0
S3 C:SF4102 2.3 34.2 1.0
S1 C:SF4102 2.3 34.5 1.0
S4 C:SF4102 2.3 33.1 1.0
SG C:CYS16 2.4 40.9 1.0
FE4 C:SF4102 2.7 35.0 1.0
FE1 C:SF4102 2.7 35.7 1.0
FE3 C:SF4102 2.7 35.5 1.0
CB C:CYS16 3.3 36.6 1.0
CB C:ALA39 3.8 34.9 1.0
N C:CYS16 3.9 39.0 1.0
S2 C:SF4102 3.9 34.1 1.0
CA C:CYS16 4.2 38.5 1.0
SG C:CYS10 4.6 35.5 1.0
SG C:CYS13 4.6 35.8 1.0
CG2 C:ILE64 4.8 29.3 1.0
N C:GLN15 4.8 39.6 1.0
CB C:ILE64 4.9 32.1 1.0
N C:THR14 4.9 33.1 1.0
SG C:CYS57 4.9 39.7 1.0
N C:VAL17 5.0 37.1 1.0

Reference:

H.N.Chapman, P.Fromme, A.Barty, T.A.White, R.A.Kirian, A.Aquila, M.S.Hunter, J.Schulz, D.P.Deponte, U.Weierstall, R.B.Doak, F.R.Maia, A.V.Martin, I.Schlichting, L.Lomb, N.Coppola, R.L.Shoeman, S.W.Epp, R.Hartmann, D.Rolles, A.Rudenko, L.Foucar, N.Kimmel, G.Weidenspointner, P.Holl, M.Liang, M.Barthelmess, C.Caleman, S.Boutet, M.J.Bogan, J.Krzywinski, C.Bostedt, S.Bajt, L.Gumprecht, B.Rudek, B.Erk, C.Schmidt, A.Homke, C.Reich, D.Pietschner, L.Struder, G.Hauser, H.Gorke, J.Ullrich, S.Herrmann, G.Schaller, F.Schopper, H.Soltau, K.U.Kuhnel, M.Messerschmidt, J.D.Bozek, S.P.Hau-Riege, M.Frank, C.Y.Hampton, R.G.Sierra, D.Starodub, G.J.Williams, J.Hajdu, N.Timneanu, M.M.Seibert, J.Andreasson, A.Rocker, O.Jonsson, M.Svenda, S.Stern, K.Nass, R.Andritschke, C.D.Schroter, F.Krasniqi, M.Bott, K.E.Schmidt, X.Wang, I.Grotjohann, J.M.Holton, T.R.Barends, R.Neutze, S.Marchesini, R.Fromme, S.Schorb, D.Rupp, M.Adolph, T.Gorkhover, I.Andersson, H.Hirsemann, G.Potdevin, H.Graafsma, B.Nilsson, J.C.Spence. Femtosecond X-Ray Protein Nanocrystallography. Nature V. 470 73 2011.
ISSN: ISSN 0028-0836
PubMed: 21293373
DOI: 10.1038/NATURE09750
Page generated: Sun Dec 13 15:17:31 2020

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