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Mercury in PDB 2d2n: Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi

Protein crystallography data

The structure of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi, PDB code: 2d2n was solved by N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.20
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 111.745, 111.745, 276.707, 90.00, 90.00, 120.00
R / Rfree (%) 24.2 / 29.7

Other elements in 2d2n:

The structure of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi (pdb code 2d2n). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi, PDB code: 2d2n:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 2d2n

Go back to Mercury Binding Sites List in 2d2n
Mercury binding site 1 out of 4 in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg500

b:63.8
occ:0.24
HG A:MMC500 0.0 63.8 0.2
SG A:CYS63 2.3 64.7 1.0
CE1 A:PHE59 2.5 66.3 1.0
CZ A:PHE59 2.5 66.3 1.0
C A:MMC500 2.7 63.8 0.2
CD1 A:PHE59 2.9 66.3 1.0
CE2 A:PHE59 3.0 66.3 1.0
CD2 A:PHE59 3.4 66.3 1.0
CG A:PHE59 3.4 66.3 1.0
O A:PHE59 3.5 56.6 1.0
CD1 A:PHE32 3.5 51.4 1.0
N A:CYS63 3.6 77.3 1.0
CB A:CYS63 3.8 64.7 1.0
CG A:PHE32 3.8 51.4 1.0
CA A:CYS63 4.0 77.3 1.0
CD2 A:HIS62 4.0 0.7 1.0
CE1 A:PHE32 4.1 51.4 1.0
CB A:HIS62 4.1 0.7 1.0
CB A:PHE32 4.1 51.4 1.0
C A:PHE59 4.1 56.6 1.0
CG A:HIS62 4.3 0.7 1.0
CB A:PHE59 4.6 66.3 1.0
CD2 A:PHE32 4.6 51.4 1.0
C A:HIS62 4.6 68.5 1.0
CA A:PHE59 4.6 56.6 1.0
CZ A:PHE32 4.8 51.4 1.0
CA A:HIS62 4.9 68.5 1.0
N A:THR60 5.0 60.3 1.0

Mercury binding site 2 out of 4 in 2d2n

Go back to Mercury Binding Sites List in 2d2n
Mercury binding site 2 out of 4 in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1500

b:68.8
occ:0.34
HG B:MMC1500 0.0 68.8 0.3
SG B:CYS73 2.2 63.8 1.0
C B:MMC1500 2.7 68.8 0.3
CD1 B:LEU90 2.9 51.3 1.0
O B:GLY69 3.5 52.5 1.0
CB B:CYS73 3.5 63.8 1.0
N B:CYS73 3.7 43.4 1.0
CE B:MET72 3.7 44.7 1.0
C B:GLY69 3.8 52.5 1.0
CA B:CYS73 3.9 43.4 1.0
CG B:LEU90 4.1 51.3 1.0
CB B:LEU86 4.3 32.6 1.0
CA B:GLY69 4.3 52.5 1.0
CD2 B:LEU90 4.3 51.3 1.0
CB B:MET72 4.3 44.7 1.0
N B:LEU70 4.4 35.0 1.0
CD2 B:LEU87 4.4 41.9 1.0
CD1 B:LEU86 4.6 32.6 1.0
C B:MET72 4.6 50.7 1.0
CA B:LEU70 4.7 35.0 1.0
N B:LEU87 4.9 36.6 1.0
C B:LEU86 5.0 46.4 1.0
CA B:MET72 5.0 50.7 1.0

Mercury binding site 3 out of 4 in 2d2n

Go back to Mercury Binding Sites List in 2d2n
Mercury binding site 3 out of 4 in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg2500

b:77.7
occ:0.38
HG C:MMC2500 0.0 77.7 0.4
C C:MMC2500 2.7 77.7 0.4
SG C:CYS67 2.7 62.4 1.0
CE2 C:PHE63 3.1 66.8 1.0
CZ C:PHE63 3.2 66.8 1.0
O C:PHE63 3.2 55.8 1.0
CD2 C:PHE63 3.3 66.8 1.0
CE1 C:PHE63 3.5 66.8 1.0
N C:CYS67 3.5 78.4 1.0
CD2 C:HIS66 3.5 96.7 1.0
CG C:PHE63 3.6 66.8 1.0
CE2 C:PHE36 3.6 54.7 1.0
CD1 C:PHE63 3.6 66.8 1.0
CD2 C:PHE36 3.7 54.7 1.0
CB C:HIS66 3.8 96.7 1.0
CA C:CYS67 3.9 78.4 1.0
CB C:CYS67 3.9 62.4 1.0
CG C:HIS66 4.0 96.7 1.0
C C:PHE63 4.0 55.8 1.0
C C:HIS66 4.2 55.3 1.0
CZ C:PHE36 4.2 54.7 1.0
CG C:PHE36 4.3 54.7 1.0
CA C:PHE63 4.4 55.8 1.0
CA C:HIS66 4.5 55.3 1.0
CB C:PHE63 4.6 66.8 1.0
CE1 C:PHE36 4.7 54.7 1.0
CD1 C:PHE36 4.7 54.7 1.0
NE2 C:HIS66 4.8 96.7 1.0
CG1 C:VAL53 4.8 64.0 1.0
O C:HIS66 4.9 55.3 1.0
N C:HIS66 4.9 55.3 1.0

Mercury binding site 4 out of 4 in 2d2n

Go back to Mercury Binding Sites List in 2d2n
Mercury binding site 4 out of 4 in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg3500

b:60.6
occ:0.55
HG D:MMC3500 0.0 60.6 0.6
CE2 D:TYR136 2.5 89.4 1.0
C D:MMC3500 2.7 60.6 0.6
SG D:CYS85 2.7 61.1 1.0
CD2 D:TYR136 3.0 89.4 1.0
CB D:CYS85 3.3 61.1 1.0
CZ D:TYR136 3.5 89.4 1.0
NH1 D:ARG82 3.6 0.1 1.0
CD2 D:LEU79 3.7 50.8 1.0
O D:LEU79 3.8 68.1 1.0
OH D:TYR136 3.9 89.4 1.0
CA D:LEU79 4.1 68.1 1.0
CZ D:ARG82 4.2 0.1 1.0
CG D:TYR136 4.3 89.4 1.0
C D:LEU79 4.4 68.1 1.0
CB D:LEU79 4.4 50.8 1.0
CD D:ARG82 4.5 0.1 1.0
NE D:ARG82 4.6 0.1 1.0
CE1 D:TYR136 4.7 89.4 1.0
CG D:LEU79 4.7 50.8 1.0
CA D:CYS85 4.8 66.1 1.0
NH2 D:ARG82 4.9 0.1 1.0
CA D:ARG82 4.9 64.7 1.0
O D:ARG82 4.9 64.7 1.0
O D:SER78 5.0 55.8 1.0
CD1 D:TYR136 5.0 89.4 1.0

Reference:

N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, K.Miki. Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi. Proc.Natl.Acad.Sci.Usa V. 102 14521 2005.
ISSN: ISSN 0027-8424
PubMed: 16204001
DOI: 10.1073/PNAS.0501541102
Page generated: Wed Oct 28 18:41:19 2020

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