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Iron in PDB 6d05: Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2.

Other elements in 6d05:

The structure of Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2. also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2. (pdb code 6d05). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2., PDB code: 6d05:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6d05

Go back to Iron Binding Sites List in 6d05
Iron binding site 1 out of 4 in the Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe701

b:74.1
occ:1.00
OH C:TYR517 2.1 68.9 1.0
O3 C:CO3702 2.1 71.8 1.0
O1 C:CO3702 2.1 71.8 1.0
NE2 C:HIS585 2.1 63.5 1.0
OH C:TYR426 2.2 74.1 1.0
C C:CO3702 2.3 71.8 1.0
NH1 C:ARG632 2.7 67.2 1.0
CE1 C:HIS585 2.9 63.5 1.0
CZ C:TYR426 3.2 74.1 1.0
CZ C:TYR517 3.3 68.9 1.0
CD2 C:HIS585 3.3 63.5 1.0
O2 C:CO3702 3.4 71.8 1.0
OG1 C:THR457 3.8 71.3 1.0
CE1 C:TYR426 3.9 74.1 1.0
CB C:ASP392 3.9 60.3 1.0
CZ C:ARG632 3.9 67.2 1.0
CE2 C:TYR426 4.0 74.1 1.0
CE1 C:TYR517 4.0 68.9 1.0
ND1 C:HIS585 4.1 63.5 1.0
CE2 C:TYR517 4.2 68.9 1.0
CG C:HIS585 4.3 63.5 1.0
OD2 C:ASP392 4.5 60.3 1.0
NE C:ARG632 4.5 67.2 1.0
NH1 C:ARG456 4.5 68.5 1.0
CG C:ASP392 4.7 60.3 1.0
NH2 C:ARG632 4.9 67.2 1.0

Iron binding site 2 out of 4 in 6d05

Go back to Iron Binding Sites List in 6d05
Iron binding site 2 out of 4 in the Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe703

b:70.8
occ:1.00
OH C:TYR95 2.1 64.9 1.0
OD1 C:ASP63 2.1 48.9 1.0
O2 C:CO3704 2.1 56.9 1.0
OH C:TYR188 2.1 66.1 1.0
NE2 C:HIS249 2.2 53.2 1.0
O3 C:CO3704 2.3 56.9 1.0
C C:CO3704 2.4 56.9 1.0
CG C:ASP63 3.0 48.9 1.0
CD2 C:HIS249 3.0 53.2 1.0
CE1 C:HIS249 3.2 53.2 1.0
CZ C:TYR95 3.4 64.9 1.0
CZ C:TYR188 3.4 66.1 1.0
OG C:SER125 3.4 52.3 1.0
OD2 C:ASP63 3.5 48.9 1.0
O1 C:CO3704 3.6 56.9 1.0
CE1 C:TYR188 4.0 66.1 1.0
CE1 C:TYR95 4.1 64.9 1.0
CB C:ASP63 4.1 48.9 1.0
CG C:HIS249 4.2 53.2 1.0
ND1 C:HIS249 4.3 53.2 1.0
CE2 C:TYR95 4.3 64.9 1.0
CE2 C:TYR188 4.5 66.1 1.0
NZ C:LYS296 4.5 70.5 1.0
NH2 C:ARG124 4.5 52.6 1.0
CA C:ASP63 4.7 48.9 1.0
CB C:SER125 4.7 52.3 1.0
CE C:LYS296 4.9 70.5 1.0

Iron binding site 3 out of 4 in 6d05

Go back to Iron Binding Sites List in 6d05
Iron binding site 3 out of 4 in the Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe701

b:71.3
occ:1.00
OH D:TYR517 2.1 68.9 1.0
O3 D:CO3702 2.1 71.8 1.0
O1 D:CO3702 2.1 71.8 1.0
NE2 D:HIS585 2.1 59.6 1.0
OH D:TYR426 2.2 72.2 1.0
C D:CO3702 2.3 71.8 1.0
NH1 D:ARG632 2.6 64.5 1.0
CE1 D:HIS585 2.9 59.6 1.0
CZ D:TYR426 3.2 72.2 1.0
CZ D:TYR517 3.3 68.9 1.0
CD2 D:HIS585 3.3 59.6 1.0
O2 D:CO3702 3.4 71.8 1.0
OG1 D:THR457 3.9 70.0 1.0
CE1 D:TYR426 3.9 72.2 1.0
CZ D:ARG632 3.9 64.5 1.0
CB D:ASP392 3.9 56.2 1.0
CE2 D:TYR426 4.0 72.2 1.0
CE1 D:TYR517 4.0 68.9 1.0
ND1 D:HIS585 4.1 59.6 1.0
CE2 D:TYR517 4.1 68.9 1.0
CG D:HIS585 4.3 59.6 1.0
NE D:ARG632 4.5 64.5 1.0
OD2 D:ASP392 4.5 56.2 1.0
NH1 D:ARG456 4.5 66.9 1.0
CG D:ASP392 4.7 56.2 1.0
NH2 D:ARG632 4.9 64.5 1.0

Iron binding site 4 out of 4 in 6d05

Go back to Iron Binding Sites List in 6d05
Iron binding site 4 out of 4 in the Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of A Plasmodium Vivax Invasion Complex Essential For Entry Into Human Reticulocytes; Two Molecules of Parasite Ligand, Subclass 2. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe703

b:72.3
occ:1.00
OH D:TYR95 2.0 61.8 1.0
O2 D:CO3704 2.1 57.3 1.0
OH D:TYR188 2.1 65.6 1.0
OD1 D:ASP63 2.1 47.1 1.0
NE2 D:HIS249 2.2 50.1 1.0
O3 D:CO3704 2.3 57.3 1.0
C D:CO3704 2.5 57.3 1.0
CG D:ASP63 3.0 47.1 1.0
CD2 D:HIS249 3.1 50.1 1.0
CE1 D:HIS249 3.2 50.1 1.0
CZ D:TYR95 3.4 61.8 1.0
CZ D:TYR188 3.4 65.6 1.0
OG D:SER125 3.4 50.0 1.0
OD2 D:ASP63 3.5 47.1 1.0
O1 D:CO3704 3.7 57.3 1.0
CE1 D:TYR188 4.0 65.6 1.0
CE1 D:TYR95 4.1 61.8 1.0
CB D:ASP63 4.2 47.1 1.0
CG D:HIS249 4.2 50.1 1.0
ND1 D:HIS249 4.3 50.1 1.0
CE2 D:TYR95 4.3 61.8 1.0
CE2 D:TYR188 4.5 65.6 1.0
NZ D:LYS296 4.5 68.4 1.0
NH2 D:ARG124 4.5 52.0 1.0
CA D:ASP63 4.7 47.1 1.0
CB D:SER125 4.7 50.0 1.0
CE D:LYS296 4.9 68.4 1.0

Reference:

J.Gruszczyk, R.K.Huang, L.J.Chan, S.Menant, C.Hong, J.M.Murphy, Y.F.Mok, M.D.W.Griffin, R.D.Pearson, W.Wong, A.F.Cowman, Z.Yu, W.H.Tham. Cryo-Em Structure of An Essential Plasmodium Vivax Invasion Complex. Nature V. 559 135 2018.
ISSN: ISSN 0028-0836
PubMed: 29950717
DOI: 10.1038/S41586-018-0249-1
Page generated: Sun Dec 13 16:23:58 2020

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