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Praseodymium in PDB 3mvc: High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans

Protein crystallography data

The structure of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans, PDB code: 3mvc was solved by J.Yoon, M.A.Herzik Jr, M.B.Winter, R.Tran, C.Olea Jr, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.70 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.582, 76.347, 62.696, 90.00, 91.76, 90.00
R / Rfree (%) 16.1 / 20.5

Other elements in 3mvc:

The structure of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Praseodymium Binding Sites:

The binding sites of Praseodymium atom in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans (pdb code 3mvc). This binding sites where shown within 5.0 Angstroms radius around Praseodymium atom.
In total 4 binding sites of Praseodymium where determined in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans, PDB code: 3mvc:
Jump to Praseodymium binding site number: 1; 2; 3; 4;

Praseodymium binding site 1 out of 4 in 3mvc

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Praseodymium binding site 1 out of 4 in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 1 of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr1

b:18.9
occ:0.34
OE2 A:GLU284 2.7 45.7 0.6
OE1 A:GLU349 2.8 44.5 1.0
O A:HOH41 2.9 31.2 1.0
OE2 A:GLU284 3.0 38.3 0.4
OE1 A:GLU284 3.0 49.3 0.4
CD A:GLU284 3.1 49.1 0.6
CD A:GLU284 3.2 47.8 0.4
OE1 A:GLU284 3.5 48.4 0.6
PR A:PR3 3.6 23.5 0.9
CD A:GLU349 3.7 35.4 1.0
CG A:GLU284 4.1 27.5 0.6
OE2 A:GLU349 4.2 31.8 1.0
CG A:GLU284 4.5 30.0 0.4
CG A:GLU349 4.8 22.8 1.0
O A:HOH38 4.9 27.2 1.0

Praseodymium binding site 2 out of 4 in 3mvc

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Praseodymium binding site 2 out of 4 in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 2 of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr2

b:15.0
occ:0.47
O A:PRO289 2.4 29.8 1.0
O A:ARG355 2.5 31.1 1.0
O A:HOH26 2.6 24.6 1.0
O A:HOH105 2.6 38.3 1.0
O A:HOH29 2.6 27.1 1.0
O2 A:NO3141 2.7 26.4 1.0
O A:HOH39 2.7 30.8 1.0
O1 A:NO3141 2.7 26.3 1.0
N A:NO3141 3.1 29.2 1.0
C A:PRO289 3.6 32.0 1.0
C A:ARG355 3.7 31.7 1.0
CA A:PRO289 4.5 24.1 1.0
CA A:ARG355 4.5 28.4 1.0
N A:THR290 4.5 24.8 1.0
O3 A:NO3141 4.5 31.6 1.0
CA A:THR290 4.6 25.2 1.0
O A:HOH23 4.6 26.5 1.0
O A:ARG354 4.8 29.9 1.0
N A:ARG291 4.8 21.0 1.0
CG A:ARG291 4.9 20.9 1.0

Praseodymium binding site 3 out of 4 in 3mvc

Go back to Praseodymium Binding Sites List in 3mvc
Praseodymium binding site 3 out of 4 in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 3 of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr3

b:23.5
occ:0.89
OE2 A:GLU284 2.5 45.7 0.6
O A:HOH41 2.6 31.2 1.0
OE2 A:GLU281 2.6 31.3 1.0
OE1 A:GLU281 2.6 35.3 1.0
OE1 A:GLU284 2.6 48.4 0.6
OE1 A:GLU284 2.7 49.3 0.4
CD A:GLU284 2.9 49.1 0.6
CD A:GLU281 3.0 35.9 1.0
PR A:PR1 3.6 18.9 0.3
CD A:GLU284 3.6 47.8 0.4
OE2 A:GLU284 3.9 38.3 0.4
O A:HOH113 4.4 36.7 1.0
CG A:GLU284 4.4 27.5 0.6
CG A:GLU281 4.5 25.9 1.0
O A:HOH120 4.7 34.3 1.0
CG A:GLU284 4.9 30.0 0.4

Praseodymium binding site 4 out of 4 in 3mvc

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Praseodymium binding site 4 out of 4 in the High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 4 of High Resolution Crystal Structure of the Heme Domain of Glb-6 From C. Elegans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pr4

b:17.5
occ:0.26
O B:PRO289 2.5 39.4 1.0
O B:HOH124 2.6 39.7 1.0
O2 B:NO3146 2.8 46.1 1.0
O1 B:NO3146 3.0 51.2 1.0
N B:NO3146 3.3 34.8 1.0
C B:PRO289 3.7 38.9 1.0
CA B:PRO289 4.5 38.5 1.0
N B:THR290 4.6 41.6 1.0
CA B:THR290 4.6 38.5 1.0
O B:HOH116 4.7 39.1 1.0
O3 B:NO3146 4.7 54.8 1.0
CG B:ARG291 4.8 45.5 1.0
N B:ARG291 4.9 27.9 1.0

Reference:

J.Yoon, M.A.Herzik, M.B.Winter, R.Tran, C.Olea, M.A.Marletta. Structure and Properties of A Bis-Histidyl Ligated Globin From Caenorhabditis Elegans. Biochemistry V. 49 5662 2010.
ISSN: ISSN 0006-2960
PubMed: 20518498
DOI: 10.1021/BI100710A
Page generated: Thu Oct 29 06:39:22 2020

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